Re: [galaxy-user] Filter Tool

[shamsher jagat]

I have shared the history with you Jeremy and has named the files
accordingly. I still have same problem and file can not be uploaded to UCSC
genome browser
by clicking icon of browser on Galaxy.
Thanks
On Mon, May 9, 2011 at 6:21 AM, Jeremy Goecks wrote:

>  (Starting new thread on galaxy-user.)
>
> Jagat,
>
> It depends what filter tool you're using and what dataset you're filtering.
> There is a generic filter tool that can be used to filter Cuffdiff tabular
> files for either FPKM values and differential expression tests. There is
> also a tool for filtering GTF files based on a Cuffdiff expr dataset. It
> sounds like you may be confusing either the tools or the inputs.
>
> If after double-checking you're still having problems with filtering,
> please put together a short list of your analysis steps and share your
> history with me, and I can take a look.
>
> Thanks,
> J.
>
>  Further to my question, It appear that there is some problem with the
> filter option:
> When I use the isoform/gene exp file as such it work fine but when I filter
> these files with either parameter such as status if test was successful or
> on p value it return me empty file. The way am saving the file is - expr
> file filter save as txt file and upload back in Galaxy.
> Any suggestion?
>
>
>
> Jagat
>
> On Tue, May 3, 2011 at 3:08 AM, shamsher jagat wrote:
>
>> Jeremy,
>>
>> I have been trying to follow  the steps in filtering Cufflink out put
>> files you have  described in one of the previous messages (
>> http://gmod.827538.n3.nabble.com/Re-downstream-analysis-of-cuffdiff-out-put-td2836457.html
>> ):
>>
>> I have shared histroy with you, but in summary:
>>
>>
>> File 35: when Filter GTF data by attributes value list on data 11
>> (combined GTF) and data 33 (which is gene expr  file) . Will not this
>> should have one gene per row. But it is not?
>>
>> File 39:  Filter GTF file by attribute value list on data 11 and data 38
>> (Cuffdiff splicing expr) it failed. I would assume that it should filter
>>  on the basis of TSSid . The error message is
>>  Traceback (most recent call last):
>>   File
>> "/var/opt/galaxy/g2test/galaxy_test/tools/filters/gff/gtf_filter_by_attribute_values_list.py",
>> line 67, in
>> filter( gff_file, attribute_name, ids_file, output_file )
>>   File
>> "/var/opt/galaxy/g2test/galaxy_test/tools/filters/gff/gtf_filter_by_attribute_values_list.py",
>> line 57, in filter
>> if attributes[ attribute_name ] in ids_dict:
>>
>> KeyError: 'tss_id'
>>
>> 40 : Filter GTF data by attribute list on data 11 and 34 (tss group exp)
>> failed and error message is:
>>
>> Traceback (most recent call last):
>>
>>   File 
>> "/var/opt/galaxy/g2test/galaxy_test/tools/filters/gff/gtf_filter_by_attribute_values_list.py",
>>  line 67, in
>>
>> filter( gff_file, attribute_name, ids_file, output_file )
>>
>>   File 
>> "/var/opt/galaxy/g2test/galaxy_test/tools/filters/gff/gtf_filter_by_attribute_values_list.py",
>>  line 57, in filter
>>
>> if attributes[ attribute_name ] in ids_dict:
>>
>> KeyError: 'tss_id'
>>
>>
>>
>> I would consider that if one gene has different Id than there is splicing
>> .
>>
>> However in contrast isoform file with transcript Id is working fine (File
>> 20)
>>
>>  On a different note can I convert GTF file to txt tab delaminated file I
>> tried to convert file 11 in txt (following Edit attributes) but the file is
>> not properly formatted especially col-pid and TSS id. Am I doing something
>> wrong.
>>
>> Thanks.
>>
>>
>
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[galaxy-user] problem with filter RNA-seq

[shamsher jagat]

I have tried to follow the steps: File 33 in my history is generated by
using  filter GTF data by attributes. Two files used were file 29 which is a
splicing diff file filtered for yes and file 2 is combined GTF. I used
TSS-id for filtering. the out put file file 32 is empty. Any suggestion?


Jagat,


It depends what filter tool you're using and what dataset you're filtering.
There is a generic filter tool that can be used to filter Cuffdiff tabular
files for either FPKM values and differential expression tests. There is
also a tool for filtering GTF files based on a Cuffdiff expr dataset. It
sounds like you may be confusing either the tools or the inputs.


If after double-checking you're still having problems with filtering, please
put together a short list of your analysis steps and share your history with
me, and I can take a look.


Thanks,
J.


Further to my question, It appear that there is some problem with the filter
option:
When I use the isoform/gene exp file as such it work fine but when I filter
these files with either parameter such as status if test was successful or
on p value it return me empty file. The way am saving the file is - expr
file filter save as txt file and upload back in Galaxy.
Any suggestion?

Jagat
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[galaxy-user] Fwd: problem with filter RNA-seq

[shamsher jagat]

Jeremy, I got it working.
Thanks
-- Forwarded message --
From: shamsher jagat o
Date: Mon, May 16, 2011 at 4:19 PM
Subject: problem with filter RNA-seq
To: jeremy.goe...@emory.edu
Cc: galaxy-u...@bx.psu.edu


I have tried to follow the steps: File 33 in my history is generated by
using  filter GTF data by attributes. Two files used were file 29 which is a
splicing diff file filtered for yes and file 2 is combined GTF. I used
TSS-id for filtering. the out put file file 32 is empty. Any suggestion?


Jagat,


It depends what filter tool you're using and what dataset you're filtering.
There is a generic filter tool that can be used to filter Cuffdiff tabular
files for either FPKM values and differential expression tests. There is
also a tool for filtering GTF files based on a Cuffdiff expr dataset. It
sounds like you may be confusing either the tools or the inputs.


If after double-checking you're still having problems with filtering, please
put together a short list of your analysis steps and share your history with
me, and I can take a look.


Thanks,
J.


Further to my question, It appear that there is some problem with the filter
option:
When I use the isoform/gene exp file as such it work fine but when I filter
these files with either parameter such as status if test was successful or
on p value it return me empty file. The way am saving the file is - expr
file filter save as txt file and upload back in Galaxy.
Any suggestion?

Jagat
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[galaxy-user] TSS list with annotation for Hg19

[shamsher jagat]

I want to extract TSS ids with correspodning  location for Hg19. Once I
extract such TSS coordinates I want to have there annotation either with
enetrz gene id or some other unique Ids. I am sure Galaxy can do this, But I
dont know where to start, or which workflow to use. Can some one please
dircet me to right dircetion. Appreciate your help.
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Re: [galaxy-user] run tophat in galaxy

[shamsher jagat]

I have related question If I have to use Ensembl mouse GTF file
(Mus_musculus.NCBIM37.64) Do I have to download and reformat it or Galaxy
can take it from the source directly?

Thanks

On Sun, Aug 28, 2011 at 8:50 AM, Peng, Tao  wrote:

>  ===> Please use "Reply All" when responding to this email! <===
>
>
> **
>
> Hi how can I specify a GTF gene annotation file when running tophat to
> guide the alignment to human genome? What is the best way to visualize the
> tophat results in the context of annotated human genome, i.e. RefSeq?
>
> Thanks,
>
> tao
>
>
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[galaxy-user] Chip-seq

[shamsher jagat]

Can I analyze two bed files from Chip seq  experiemnt in Galaxy? I have one
file of input and other of sample. Both these files have peak locations. Any
suggestion of a work flow in Galaxy?
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[galaxy-user] BED to BAM conversion in Galaxy

[shamsher jagat]

Is it possible to use some tool in Galaxy to convert BED file to Bam/ sam
file. In other word do we have Bed tools or other option in Galaxy

Thanks
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[galaxy-user] mm9 reference GTF file for Cuffcompare

[shamsher jagat]

I wonder if some has mouse genome GTF file compatible with Tophat/
Cuffcompare. The contig names on  Ensembel and that of Tophat GTF file are
not same.
Thanks
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Re: [galaxy-user] BED to BAM conversion in Galaxy

[shamsher jagat]

Thanks Jen,

My problem is I have ChIP-seq data where I have one Bed
file with  coordinates-


chr1   724027  724226  61PDWAAXX100706:4:19:6952:18071   -

Then there is wig file.? Is it possible that thsi data can be analyzed in
Galaxy/ Cistrome. I tried to use Cistrome  which gav eme error message.



Thanks


On Wed, Sep 28, 2011 at 3:46 PM, Jennifer Jackson  wrote:

> Hello,
>
> It is possible to go from SAM/BAM to BED, but not the reverse. SAM/BAM
> files contain the actual sequence data associated with the original aligned
> read. BED files only have the reference genome location of the alignment (no
> read "sequence").
>
> It is possible to extract genomic sequence based on BED coordinates, but
> the resulting sequence would not necessarily be the same sequence as in the
> original aligned read (any variation would be lost).
>
> BED is very similar to Interval format, so Interval tools also work with
> BED format. A BED file is basically a 3-12 column, tab delimited file, so
> tools that work with Tabular data are also appropriate for BED file. Note
> that you may need to change the datatype to be interval or tab for certain
> tools to recognize a BED file as an input.
>
> Hopefully this helps,
>
> Jen
> Galaxy team
>
>
>
>
> On 9/22/11 2:55 PM, shamsher jagat wrote:
>
>>  Is it possible to use some tool in Galaxy to convert BED file to Bam/
>> sam file. In other word do we have Bed tools or other option in Galaxy
>>
>> Thanks
>>
>>
>> __**_
>> The Galaxy User list should be used for the discussion of
>> Galaxy analysis and other features on the public server
>> at usegalaxy.org.  Please keep all replies on the list by
>> using "reply all" in your mail client.  For discussion of
>> local Galaxy instances and the Galaxy source code, please
>> use the Galaxy Development list:
>>
>>   
>> http://lists.bx.psu.edu/**listinfo/galaxy-dev<http://lists.bx.psu.edu/listinfo/galaxy-dev>
>>
>> To manage your subscriptions to this and other Galaxy lists,
>> please use the interface at:
>>
>>   http://lists.bx.psu.edu/
>>
>
> --
> Jennifer Jackson
> http://usegalaxy.org
> http://galaxyproject.org/**Support <http://galaxyproject.org/Support>
>
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Re: [galaxy-user] BED to BAM conversion in Galaxy

[shamsher jagat]

This is what I followed:


1.   Upload the Bed file (60) > Text manipulation Add column –add this
value 0; iterate –no will give  file 73

2.   73 >  Txt manipulation – cut > c1,c2,c3,c4,c6,c5 and delimited by
tab-  give file 74

3.   74> pencil icon>  change data type – tabular – file 74

4.   Txt manipulation- Convert  all white spaces to tab – 75

5.   *Condense consecutive characters- don’t find this option-  I am
using Dev. Galaxy version Is it somehow possible this option in develop
option*

6.   Change file type – BED file 75

7.   Pencil> edit attribute col 5 for score- file 75

8.   Run MACS from NGS peak calling-
I have shared my history with you please (http://test.g2.bx.psu.edu/root)
How we can annotate the genes corresponding to peaks.
Thanks

On Fri, Sep 30, 2011 at 7:08 AM, Jennifer Jackson  wrote:

> Hello,
>
> The format of the BED file may be a problem. To be in BED format, an
> additional field is required for the "score" attribute. This would be column
> 5, moving the strand out to column 6.
>
> To do this:
>
> 1 - use "Text Manipulation->Add column" with the value "0"
> note: "0" often is used to represent a NULL or undefined score value in BED
> files. This field cannot be left as whitespace (two tabs), a placeholder
> value must be present.
>
> 2 - then use ""Text Manipulation->Cut" and cut out the columns in the
> proper BED file order, in this case "c1,c2,c3,c4,c6,c5", to swap the last
> two
>
> 3 - change datatype to BED using the pencil icon/Edit attributes form
>
> In Galaxy, many of the tools in "NGS: Peak Calling" will work with ChIP-seq
> data in BED format. Having a control would be helpful, but is not required
> by all tools.
>
> Good luck with your project,
>
> Jen
> Galaxy team
>
>
> On 9/29/11 9:31 PM, shamsher jagat wrote:
>
>> Thanks Jen,
>> My problem is I have ChIP-seq data where I have one Bed
>> file with  coordinates-
>>
>> chr172402772422661PDWAAXX10070**6:4:19:6952:18071-
>>
>> Then there is wig file.? Is it possible that thsi data can be analyzed
>> in Galaxy/ Cistrome. I tried to use Cistrome  which gav eme error message.
>>
>> Thanks
>>
>>
>>
>> On Wed, Sep 28, 2011 at 3:46 PM, Jennifer Jackson > <mailto:j...@bx.psu.edu>> wrote:
>>
>>Hello,
>>
>>It is possible to go from SAM/BAM to BED, but not the reverse.
>>SAM/BAM files contain the actual sequence data associated with the
>>original aligned read. BED files only have the reference genome
>>location of the alignment (no read "sequence").
>>
>>It is possible to extract genomic sequence based on BED coordinates,
>>but the resulting sequence would not necessarily be the same
>>sequence as in the original aligned read (any variation would be lost).
>>
>>BED is very similar to Interval format, so Interval tools also work
>>with BED format. A BED file is basically a 3-12 column, tab
>>delimited file, so tools that work with Tabular data are also
>>appropriate for BED file. Note that you may need to change the
>>datatype to be interval or tab for certain tools to recognize a BED
>>file as an input.
>>
>>Hopefully this helps,
>>
>>Jen
>>Galaxy team
>>
>>
>>
>>
>>On 9/22/11 2:55 PM, shamsher jagat wrote:
>>
>>Is it possible to use some tool in Galaxy to convert BED file to
>>Bam/
>>sam file. In other word do we have Bed tools or other option in
>>Galaxy
>>
>>Thanks
>>
>>
>>__**__**_
>>
>>The Galaxy User list should be used for the discussion of
>>Galaxy analysis and other features on the public server
>>at usegalaxy.org <http://usegalaxy.org/>.  Please keep all
>>
>>replies on the list by
>>using "reply all" in your mail client.  For discussion of
>>local Galaxy instances and the Galaxy source code, please
>>use the Galaxy Development list:
>>
>>
>> http://lists.bx.psu.edu/__**listinfo/galaxy-dev<http://lists.bx.psu.edu/__listinfo/galaxy-dev>
>>
>>
>> <http://lists.bx.psu.edu/**listinfo/galaxy-dev<http://lists.bx.psu.edu/listinfo/galaxy-dev>
>> >
>>
>>To manage your subscriptions to this and other Galaxy lists,
>>please use the interface at:
>>
>>  

Re: [galaxy-user] BED to BAM conversion in Galaxy

[shamsher jagat]

Now when I run the same files in the main Galaxy server it gave me following
errors, Do you have any suggestion how these same files will be working ion
Develop server but not on main server using same steps.

INFO @ Tue, 04 Oct 2011 14:56:21: # ARGUMENTS LIST: # name = MACS_in_Galaxy
# format = BED # ChIP-seq file =
/galaxy/main_database/files/003/068/dataset_3068865.dat # control file =
/galaxy/main_database/files/003/068/dataset_3068668.dat # effective genome
size = 2.70e+09 # tag size = 25 # band width = 300 # model fold = 30 #
pvalue cutoff = 5.00e-02 # Ranges for calculating regional lambda are :
peak_region,1000,5000,1 INFO @ Tue, 04 Oct 2011 14:56:21: #1 read tag
files... INFO @ Tue, 04 Oct 2011 14:56:21: #1 read treatment tags... INFO @
Tue, 04 Oct 2011 14:56:32: 100 INFO @ Tue, 04 Oct 2011 14:56:44: 200
INFO @ Tue, 04 Oct 2011 14:56:55: 300 INFO @ Tue, 04 Oct 2011 14:57:06:
400 INFO @ Tue, 04 Oct 2011 14:57:19: 500 INFO @ Tue, 04 Oct 2011
14:57:30: 600 INFO @ Tue, 04 Oct 2011 14:57:41: 700 INFO @ Tue, 04
Oct 2011 14:57:52: 800 INFO @ Tue, 04 Oct 2011 14:58:03: 900 INFO @
Tue, 04 Oct 2011 14:58:15: 1000 INFO @ Tue, 04 Oct 2011 14:58:26:
1100 INFO @ Tue, 04 Oct 2011 14:58:37: 1200 INFO @ Tue, 04 Oct 2011
14:58:49: #1.2 read input tags... Traceback (most recent call last): File
"/home/g2main/linux2.6-x86_64/bin/macs", line 273, in main() File
"/home/g2main/linux2.6-x86_64/bin/macs", line 57, in main (treat, control) =
load_tag_files_options (options) File
"/home/g2main/linux2.6-x86_64/bin/macs", line 256, in load_tag_files_options
control = options.build(open2(options.cfile, gzip_flag=options.gzip_flag))
File "/home/g2main/linux2.6-x86_64/lib/python2.6/MACS/IO/__init__.py", line
1063, in build_fwtrack (chromosome,fpos,strand) =
self.__fw_parse_line(thisline) File
"/home/g2main/linux2.6-x86_64/lib/python2.6/MACS/IO/__init__.py", line 1102,
in __fw_parse_line raise self.StrandFormatError(thisline,thisfields[5])
MACS.IO.StrandFormatError: 'Strand information can not be recognized in this
line: "chr1\t10093\t10093\t10292\t61PDWAAXX100706:4:82:5766:21319

I  can share this history if required please.
Thanks.

On Mon, Oct 3, 2011 at 3:58 PM, shamsher jagat  wrote:

> This is what I followed:
>
>
> 1.   Upload the Bed file (60) > Text manipulation Add column –add this
> value 0; iterate –no will give  file 73
>
> 2.   73 >  Txt manipulation – cut > c1,c2,c3,c4,c6,c5 and delimited by
> tab-  give file 74
>
> 3.   74> pencil icon>  change data type – tabular – file 74
>
> 4.   Txt manipulation- Convert  all white spaces to tab – 75
>
> 5.   *Condense consecutive characters- don’t find this option-  I am
> using Dev. Galaxy version Is it somehow possible this option in develop
> option*
>
> 6.   Change file type – BED file 75
>
> 7.   Pencil> edit attribute col 5 for score- file 75
>
> 8.   Run MACS from NGS peak calling-
> I have shared my history with you please (http://test.g2.bx.psu.edu/root)
> How we can annotate the genes corresponding to peaks.
> Thanks
>
> On Fri, Sep 30, 2011 at 7:08 AM, Jennifer Jackson  wrote:
>
>> Hello,
>>
>> The format of the BED file may be a problem. To be in BED format, an
>> additional field is required for the "score" attribute. This would be column
>> 5, moving the strand out to column 6.
>>
>> To do this:
>>
>> 1 - use "Text Manipulation->Add column" with the value "0"
>> note: "0" often is used to represent a NULL or undefined score value in
>> BED files. This field cannot be left as whitespace (two tabs), a placeholder
>> value must be present.
>>
>> 2 - then use ""Text Manipulation->Cut" and cut out the columns in the
>> proper BED file order, in this case "c1,c2,c3,c4,c6,c5", to swap the last
>> two
>>
>> 3 - change datatype to BED using the pencil icon/Edit attributes form
>>
>> In Galaxy, many of the tools in "NGS: Peak Calling" will work with
>> ChIP-seq data in BED format. Having a control would be helpful, but is not
>> required by all tools.
>>
>> Good luck with your project,
>>
>> Jen
>> Galaxy team
>>
>>
>> On 9/29/11 9:31 PM, shamsher jagat wrote:
>>
>>> Thanks Jen,
>>> My problem is I have ChIP-seq data where I have one Bed
>>> file with  coordinates-
>>>
>>> chr172402772422661PDWAAXX10070**6:4:19:6952:18071-
>>>
>>> Then there is wig file.? Is it possible that thsi data can be analyzed
>>> in Galaxy/ Cistrome. I tried to use Cistrome  which gav eme error
>>> message.
>

[galaxy-user] Question about formattung mouse (mm9) GTF

[shamsher jagat]

I have read in the mailing list that you have a workflow  which can modify
the human GTF file so that it will be compatible with Top Hat. Will it also
work with Ensembl mm9 GTF or there is a different work flow.

Thanks
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[galaxy-user] Bed to Wiggle?

[shamsher jagat]

Is there an option to convert Bed file to wiggle file in Galaxy?

Thanks
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[galaxy-user] Data gets deleted from public server

[shamsher jagat]

I uploaded two BAM files and was working with them but when I tried to use
them again they are automatically deleted along with all the steps
of analysis?
Any reason or I am missing something.

Shamsher
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Re: [galaxy-user] Data gets deleted from public server

[shamsher jagat]

Yes I was and infect when I logged out and logged in back it was there then
I left for lunch and when I come back data is not there? It is weird.
Shamsher


On Mon, Nov 7, 2011 at 5:00 PM, Nate Coraor  wrote:

> On Nov 7, 2011, at 7:11 PM, shamsher jagat wrote:
>
> > I uploaded two BAM files and was working with them but when I tried to
> use them again they are automatically deleted along with all the steps of
> analysis?
> > Any reason or I am missing something.
>
> Hi Shamsher,
>
> Were you logged in when you performed this analysis?
>
> --nate
>
> >
> > Shamsher
> > ___
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Re: [galaxy-user] Data gets deleted from public server

[shamsher jagat]

Could you direct me how I can save history from a series of steps I have
performed in Galaxy and can later use the same work flow steps. I think
this is what is happening when I logged in back there were two windows open
with my log in info

Thanks

Shamsher

On Tue, Nov 8, 2011 at 5:36 AM, Jennifer Jackson  wrote:

> Hi Shamsher,
>
> Are you by chance working with more than one open Galaxy browser window at
> a time? Doing this is not recommended as it can cause confusing results
> between the histories. Instead, move between histories using the "Options
> -> Saved Histories" form, in a single browser window.
>
> Please let us know if you are still having problems,
>
> Best,
>
> Jen
> Galaxy team
>
>
>
> On 11/7/11 5:53 PM, shamsher jagat wrote:
>
>> Yes I was and infect when I logged out and logged in back it was there
>> then I left for lunch and when I come back data is not there? It is weird.
>> Shamsher
>>
>>
>> On Mon, Nov 7, 2011 at 5:00 PM, Nate Coraor > <mailto:n...@bx.psu.edu>> wrote:
>>
>>On Nov 7, 2011, at 7:11 PM, shamsher jagat wrote:
>>
>> > I uploaded two BAM files and was working with them but when I
>>tried to use them again they are automatically deleted along with
>>all the steps of analysis?
>> > Any reason or I am missing something.
>>
>>Hi Shamsher,
>>
>>Were you logged in when you performed this analysis?
>>
>>--nate
>>
>> >
>> > Shamsher
>> > __**_
>> > The Galaxy User list should be used for the discussion of
>> > Galaxy analysis and other features on the public server
>> > at usegalaxy.org <http://usegalaxy.org>.  Please keep all replies
>>
>>on the list by
>> > using "reply all" in your mail client.  For discussion of
>> > local Galaxy instances and the Galaxy source code, please
>> > use the Galaxy Development list:
>> >
>> > 
>> http://lists.bx.psu.edu/**listinfo/galaxy-dev<http://lists.bx.psu.edu/listinfo/galaxy-dev>
>> >
>> > To manage your subscriptions to this and other Galaxy lists,
>> > please use the interface at:
>> >
>> > http://lists.bx.psu.edu/
>>
>>
>>
>>
>> __**_
>> The Galaxy User list should be used for the discussion of
>> Galaxy analysis and other features on the public server
>> at usegalaxy.org.  Please keep all replies on the list by
>> using "reply all" in your mail client.  For discussion of
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>>
>>   
>> http://lists.bx.psu.edu/**listinfo/galaxy-dev<http://lists.bx.psu.edu/listinfo/galaxy-dev>
>>
>> To manage your subscriptions to this and other Galaxy lists,
>> please use the interface at:
>>
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>
> --
> Jennifer Jackson
> http://usegalaxy.org
> http://galaxyproject.org/wiki/**Support<http://galaxyproject.org/wiki/Support>
>
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[galaxy-user] CEAS in Galaxy

[shamsher jagat]

Is there an option of running CEAS tool in Galaxy I want to annotate
selected enriched  regions of ChIP seq data with gene names etc?

Thanks
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Re: [galaxy-user] TopHat/Cufflinks visualization

[shamsher jagat]

Ues IGV  or Galaxy tracker.


On Wed, Nov 9, 2011 at 9:37 AM, Alessia D  wrote:

> How do people on this mailing list usually visualize Tophat and/or
> Cufflinks results (eg. tracks on UCSC browser)?
>
> I have only this once before, and I started with a .wig file that I
> uploaded to the genome browser, however it looks like Tophat does not give
> any .wig file in the output.  Suggestions?
>
> Thanks!
>
> A
>
>
>
>
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[galaxy-user] MA2C peak calling or nimbelgen chip on chip analysis

[shamsher jagat]

Do we have option of running MA2C peaks in Galaxy or is tehre an option of
analyzing Chip on Chip data from Nimbelgen.

Thanks
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Re: [galaxy-user] RV: Visual and Conputational Analysis of positive sites in chip-chip data

[shamsher jagat]

I dont think Cistrome can provide sufficient visualization options. In CEAS
analysis it can provide overall picture of genome binding regions or some
relative binding histograms. I beleive what Monica is asking when one has
chip enriched regions how to visualize such selected regions- I will
suggest IGV or loading file to UCSC genome browser. However It will
be interesting if either some one from Galaxy/ Cistrome (Tau/ Shirley) can
add to this post as personally it may be easy to do everything in cistrome/
Galaxy rather then flipping files between various tools.

Best

2011/11/16 Abhay Krishna 

> I think closest to what you want to do in galaxy can be done in cistrome
>
> http://wiki.g2.bx.psu.edu/Community/Cistrome
>
>
> Unless I am missing some galaxy tool in testing, which other galaxy users
> more closely following galaxy test can comment on
>
> best
> Abhay
>
>
>
> 2011/11/16 Mónica Pérez Alegre 
>
>> **
>>
>> Hi all
>>
>> ** **
>>
>> We are working with chip-chip data of S. *cerevisiae* (from Affymetrix)
>> and actually we have two problems and we don´t know if it´s possible to
>> perform in Galaxy:
>>
>> ** **
>>
>>1. We use the tool intersect to get the annotation of positive
>>genomic regions in our file bed. After, we need calculate statistical
>>enrichments for associations between genomics regions and annotations. 
>> It´s
>>this possible in Galaxy?
>>2. Other query. How plot for visual inspection enrichment ratio
>>profile versus different sets of genomic loci (i.e.: tRNA, LTR,…)
>>
>> ** **
>>
>> Best Regards,
>>
>> ** **
>>
>> *☺**If you have used the Services of the Genomics Unit** **of Cabimer,
>> we would be grateful if you would give us a mention in future publications
>> ***
>>
>> ***Mónica Pérez Alegre, PhD***
>>
>> *Genomics Unit*
>>
>> *CABIMER-CSIC***
>>
>> *Edif. CABIMER - Avda. Américo Vespucio s/n***
>>
>> *Parque Científico y Tecnológico Cartuja 93***
>>
>> *41092 Seville-SPAIN*
>>
>> *Tlf:   +34 954 467 828***
>>
>> *Fax: +34 954 461 664***
>>
>> *www.cabimer.es*
>>
>> *http://www.cabimer.es/web/es/unidades-apoyo/genomica*
>> 
>>
>> ** **
>>
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[galaxy-user] tools for exome sequence

[shamsher jagat]

Is there any tool (work flow) in galaxy for exome sequence analysis (human/
mouse)

Thanks.
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[galaxy-user] small RNA analysis

[shamsher jagat]

I posted this question previously- IS there any work flow for analysis of
microRNA/ small RNA in galaxy, please. I have run microRNA sequencing for
control and treated cells.

Thanks
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[galaxy-user] Question about plotting circos plot

[shamsher jagat]

I wonder if is it possible to visualize mutation data in circular plot
termed as circos plot e.g
 @http://www.eurekalert.org/multimedia/pub/31019.php?from=181881

Any suggestion for an alternative tool will also be appreciated.


Thanks

Shamsher
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[galaxy-user] Fwd: Question about plotting circos plot

[shamsher jagat]

My apology for re-posting the same question however I believe my first
message was returned.


I wonder if is it possible to visualize mutation data in circular plot
termed as circos plot e.g
 @http://www.eurekalert.org/multimedia/pub/31019.php?from=181881

Any suggestion for an alternative tool will also be appreciated.


Thanks

Shamsher
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[galaxy-user] BWA in Galaxy

[shamsher jagat]

Is it possible to align FASTq reads from Illumina Hi-seq reads to human
genome in Galaxy? I see only Bowtie/ I guess next question will be how
different is Bowtie from BWA?
I want to find out sequence variations.
Thanks
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[galaxy-user] Question about megablast

[shamsher jagat]

I have a question about megablast, I want to megablast my seq:
the databases mentioned include (against target databases):
htgs27
nt27
wgs 09
phiX174

How can I find details about these databases and which one is human or
mouse or may be best for my case.


Thanks

Vasu
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[galaxy-user] Megablast question

[shamsher jagat]

Hi,
I am using megablast and was wondering how can I get chromosome number
and coordinates of its hits.

Thanks

Shamesher
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[galaxy-user] Can we change - bwasw command in Galaxy

[shamsher jagat]

I am doing alignments of 454 reads in bwa and was wondering if there is an
option to change it to bwasw and use Galaxy web version?

Thanks
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[galaxy-user] Question about Samtools filter in Galaxy

[shamsher jagat]

I have a sam file after running BWASW and want to extract unique
(alignments that are aligning once to genome) from this sam file. I read in
other posts that I may be able to use Sam tools> filter Sam option to
filter the said flag on wise flag. However I could not find whether I have
to use default setting of column 2? when I use option of add flags there
are different options for pair reads, however my data is single reads. So
exactly single read alignments sam file how we extract unique reads.
Am I missing something. I can also share history  in order to explain my
point if required.

Thanks

Kanwar
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[galaxy-user] Fwd: Question about Samtools filter in Galaxy

[shamsher jagat]

My apology for reposting my questions. I posted this question last week aan
helpnd wonder if some one can help me in this?
Thanks

-- Forwarded message --
From: shamsher jagat 
Date: Wed, Apr 25, 2012 at 7:38 AM
Subject: Question about Samtools filter in Galaxy
To: galaxy-user 
Cc: Jennifer Jackson 


I have a sam file after running BWASW and want to extract unique
(alignments that are aligning once to genome) from this sam file. I read in
other posts that I may be able to use Sam tools> filter Sam option to
filter the said flag on wise flag. However I could not find whether I have
to use default setting of column 2? when I use option of add flags there
are different options for pair reads, however my data is single reads. So
exactly single read alignments sam file how we extract unique reads.
Am I missing something. I can also share history  in order to explain my
point if required.

Thanks

Kanwar
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[galaxy-user] FASTq sanger to Illumina FASTq

[shamsher jagat]

I want to convert Sanger FASTq to Illumina FASTq with a understanding that
Sanger is the current option with CASAVA. Is it possible to do
such conversion in Galaxy?

Thanks
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[galaxy-user] Question about extracting information from CEAS run results

[shamsher jagat]

I have run a ChIPseq work flow in galaxy, At teh end I ran CEAS: Enrichment
on chromosome and annotation (version 1.0.0) to annotate the peaks
which gave me a pdf file shoiwng distribution of peaks across genome with
pie chart as well as well as histogram. It shows that ~5% of my peaks in
5UTR regions and other 3 % in 3' UTR 63 % exon and so on. Is there a way
that I can have list of genes/ refrence ids  which arein 5'UTR /3'UTR. I
tried all tools in Galaxy but could not find it. There should be some way
to extract these summarized results in details. Any one has a suggestion
please?

Thanks

Kanwar
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[galaxy-user] How to transfer files between two galaxy instances

[shamsher jagat]

I have uploaded files in citsrome/  Gunner Ratch lab Galaxy instances which
allow users to use their tool. I want to either share work flow from these
instances or atleast transfer FAstq files to penn state open source
galaxy severer. Is it possible or not?

I have another question in this regard when I tried to upload the FASTq
files via web link or FTP the job is never completed. I  have tried it
couple of times. This problem is there from last couple of months. Are
there so me changes which have been implemented recently which is not
allowing me to upload the files. Indeed I have seen from last month or so
too many messages suggesting either Tophat job stuck or job is not
completed or unable to upload the file. I am not if all tehse problems are
related (storage) or not. Can someone from Galaxy team advice.
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Re: [galaxy-user] How to transfer files between two galaxy instances

[shamsher jagat]

Thanks Jen for the update. I tried following:
Go to Ratsch Galaxy instance > workflow> make work flow accessible via link
Go to galaxy Penn server
Workflow> import workflow URL> galaxy UR

error is
 The data content does not appear to be a Galaxy workflow.
Exception: No JSON object could be decoded: line 1 column 0 (char 0)

I also downloaded the file from Ratsch serever saved on computer and  use
option of Choose file under import galaxy flow it importe dthe file afetr a
while and when I opened workflow there was no data only steps of the
workflow were there.

Do you have any suggestion wheer I am doing something wrong.

Thanks



On Thu, May 24, 2012 at 8:13 AM, Jennifer Jackson  wrote:

> Hi again,
>
> I have an important update - I was incorrect about workflow transfer
> between Galaxy instances and where to edit. In summary, it is important to
> do the workflow editing up-front before the export, instead of after
> import. I'll explain why.
>
> While it is now possible to import workflows from other Galaxy instances
> (any), once actually in that new instance, if that workflow contains tools
> that are not in the new target instance, there is nothing that can be done
> with it (editing or running will result in a server error). This is a known
> open issue with the workflow developers.
>
> So, when you plan to import into the public main Galaxy instance, you will
> need to modify any workflow in the source instance before exporting it to
> make certain that it only contains tools that are present in the public
> main Galaxy instance. If a server error results from an imported workflow,
> an unavailable tool present in the workflow is the most likely root cause
> of the problem.
>
> If you plan to import into a local or cloud instance, then you have the
> choice of either modifying the workflow and/or adding all of the workflow
> tools to your local/cloud instance, and then importing the workflow. You do
> not import the workflow first as this will result in an error - if it
> occurs, delete the workflow and import again after the required tools are
> added.
>
> Good question and I apologize for getting this detail incorrect in the
> original reply.
>
> Best,
>
> Jen
> Galaxy team
>
>
> On 5/23/12 10:06 PM, Jennifer Jackson wrote:
>
> Hello,
>
> On 5/23/12 7:30 PM, shamsher jagat wrote:
>
> I have uploaded files in citsrome/  Gunner Ratch lab Galaxy instances
> which allow users to use their tool. I want to either share work flow from
> these instances or atleast transfer FAstq files to penn state open source
> galaxy severer. Is it possible or not?
>
> Incorrect start -->>
>
> It would not be possible to share a workflow between two Galaxy instance
> using the built in "Share or Publish" methods, however, you should be able
> to download a workflow from one Galaxy instance and then "Upload or import
> workflow" into the public main Galaxy instance (this button is on the
> "Workflow" home page). Please note that any tools included in your workflow
> that were available in the other instance, but that are not available on
> the public main Galaxy instance, would not be functional, so the workflow
> will likely need to be edited before use.
>
> << -- Incorrect end, see above
>
>
> Moving FASTQ datasets from other instances should also be straightforward
> - download, then upload these to the public main Galaxy instance using FTP.
> If you are having trouble downloading workflows or datasets, then the host
> Galaxy instance should be contacted.
>
>
> I have another question in this regard when I tried to upload the FASTq
> files via web link or FTP the job is never completed. I  have tried it
> couple of times. This problem is there from last couple of months. Are
> there so me changes which have been implemented recently which is not
> allowing me to upload the files. Indeed I have seen from last month or so
> too many messages suggesting either Tophat job stuck or job is not
> completed or unable to upload the file. I am not if all tehse problems are
> related (storage) or not. Can someone from Galaxy team advice.
>
> At this time, there are no known issues with upload functions.  If you are
> having problems with URL data transfer from another Galaxy instance (or
> really, any 3rd party source), you can try to download the data locally to
> your desktop in a terminal prompt (as a test) with the command:
>
> % curl -O
> 'copied_link_location_from_dataset_history_or_workflow_or_other_URL'
>
> If this is successful, then a load into Galaxy should be successful. If
> this is unsuccessful, first contact the source to check if the data is
> publicly accessible, as they may hav

Re: [galaxy-user] How to transfer files between two galaxy instances

[shamsher jagat]

Ok. Perhaps I am not understanding the process- I am not making any head
way in transfering the data from one Galaxy instance to other. I have
uploaded some files in Rutsch lab galaxy instance and have url
http://galaxy.tuebingen.mpg.de/workflow/for_direct_import?id=9b305a114b324ccf

Nothing is happening. Is it possible that some one from Galaxy team can
enlist steps of - how to transfer files (data) from one galaxy instance to
other please, considering me as a beginer. Thanks. Sorry for pushing this
question.

Vasu
On Fri, May 25, 2012 at 11:33 AM, Dannon Baker  wrote:

>  Hi,
>
> Just wanted to add a few clarifications here.  It definitely *is*
> currently possible to transfer a workflow from one instance to another
> instance that does not have (some or all) of the tools for a particular
> workflow.
>
> The error you're running into "No JSON object" means that you likely have
> the wrong link to your workflow.  The one you want is accessible via the
> workflow context menu -> Download or Export -> URL for importing into
> another galaxy.  Or, you could just download the raw file if you want and
> upload that as you figured out.  The format of the correct URL should look
> like this, note the "for_direct_import" in the string:
>
> https://main.g2.bx.psu.edu/workflow/for_direct_import?id=53b7bf0869d3e7ee
>
> As a correction to what was previously said, I would not recommend
> stripping out tools from an existing workflow prior to export.  When you
> upload the workflow to a new instance, if tools aren't available you will
> see something like the following when you edit the workflow, which
> specifies that the tool is not found:
>
>
> And at this point the unrecognized tools can be installed if it's your
> galaxy server, or if you wish, removed from the workflow via the editor.
>  This must be done before the workflow will be usable.
>
> Lastly, workflows don't contain any data, just the organization and
> parameters of steps for a process.  What it sounds like you're looking for
> (to get your data there as well) is a history export, which is available
> through the menu at the top of your history as "Export to File".
>
> -Dannon
>
>
> On May 24, 2012, at 4:06 PM, shamsher jagat wrote:
>
> Thanks Jen for the update. I tried following:
> Go to Ratsch Galaxy instance > workflow> make work flow accessible via link
> Go to galaxy Penn server
> Workflow> import workflow URL> galaxy UR
>
> error is
>  The data content does not appear to be a Galaxy workflow.
> Exception: No JSON object could be decoded: line 1 column 0 (char 0)
>
> I also downloaded the file from Ratsch serever saved on computer and  use
> option of Choose file under import galaxy flow it importe dthe file afetr a
> while and when I opened workflow there was no data only steps of the
> workflow were there.
>
> Do you have any suggestion wheer I am doing something wrong.
>
> Thanks
>
>
>
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[galaxy-user] Converting to index files of viral genome for running TopHAT

[shamsher jagat]

I was wondering if it is some how possible in galaxy to format FAST genome
seq file of microbial genome to format to generate bowtie index so that it
can be used for RNA seq analysis using TopHat.  Alternatively any pointer
to an available tool which can generate index files.

Thanks


Kanwar
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Re: [galaxy-user] "job is waiting to run" forever

[shamsher jagat]

I brought up this issue previously, I guess Galaxy team please look into it
your user base is expending the jobs never get fisnished. Fisrt problem of
data uplaod and then running jobs. I never had problem but having lot of
problem sfrom last 3-4 months so started using other tools too.

Thanks

On Mon, Jul 9, 2012 at 1:17 AM, Yehoshua Enuka  wrote:

> Dear Sir/Madam,
>
> I am a registered user of the public Galaxy Server (main). Any job I
> submitted today is labeled as "Job is waiting to run" forever. Could you
> please let me know the
> possible reasons?
>
> Sincerely,
>
> Enuka
>
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[galaxy-user] Question about SICER out put

[shamsher jagat]

I used SICR to call peaks  and have  following out put files:

1. test.1removed bed
2. control1 removed .bed
3. test w 200 graph
4. test w200 normalized graph
5. test w200-G600 FDR.05 island.bed
6. test w200-G600 FDR .05 island filtered.bed
7. test w200-G600 FDR .05 island filtered normalized.wig
8. test w200-G600 FDR.05 score island
9. test w200-G600 summary  island

Which of these files should be used. I think file 5 and 6 are the ones for
visualization as well for annotating with genomic regions. I have read the
original paper but it is not very clear what these out puts mean. Could
some one please guide me what these files mean and what is useful and rest
are intermediate files.

My second question is authors of SICER has emphasized about teh importance
of choosing gap size and window size. gap size they mention 1-3 -5
depending upon the peak distribution, but I see in Galaxy the default is
600 gap size do we need to change it to 1,2- 5 or I am missing something.

Any advise please but I did my searching on net.

Thanks
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[galaxy-user] flaking regions across TSS

[shamsher jagat]

I am interested in getting regions flanking TSS, I am using Glaxaxy and
have downloaded TSS sites using
this post steps
https://lists.soe.ucsc.edu/pipermail/genome/2011-June/026175.html

Now what I would like to do is to get 5000 bp upstream an
downstream using flank tool in galaxy, but i realize it only gave me option
for gene start or whole gene.
Is it possible to extract 5000 bp upstream and downstream regions across
tss start site . Once I have that then I want to find non overlaping genes
in my regions from chipseq data.

Thanks

Kanwar
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Re: [galaxy-user] flaking regions across TSS

[shamsher jagat]

I want to have list of genes from UCSC browser or known genes.

Thanks

Kanwar

On Fri, Jul 20, 2012 at 8:00 PM, Jennifer Jackson  wrote:

> Hello Kanwar,
>
>
> On 7/20/12 3:31 PM, shamsher jagat wrote:
>
>> I am interested in getting regions flanking TSS, I am using Glaxaxy and
>> have downloaded TSS sites using
>> this post steps
>> https://lists.soe.ucsc.edu/**pipermail/genome/2011-June/**026175.html<https://lists.soe.ucsc.edu/pipermail/genome/2011-June/026175.html>
>>
>> Now what I would like to do is to get 5000 bp upstream an
>> downstream using flank tool in galaxy, but i realize it only gave me
>> option for gene start or whole gene.
>>
>
> The "Region:" options are:
> 1 - around start - meaning interval start coordinate
> 2 - around end - meaning interval end coordinate
> 3 - whole gene - meaning entire intervals
>
> Pick option #1.
>
>
>  Is it possible to extract 5000 bp upstream and downstream regions across
>> tss start site .
>>
>
> The "Location of the flanking region/s:" options are:
> 4 - Upstream
> 5 - Downstream
> 6 - Both
>
> Pick option #6 with "Length of the flanking region(s):" set to 5000.
>
>
> Once I have that then I want to find non overlaping
>
>> genes in my regions from chipseq data.
>>
>
> Do you want to identify/label known genes or discover novel genes? This
> part of your question is not clear. Could you explain in more detail the
> end goal?
> It is likely some for of the tool "Operate on Genomic Intervals - > Merge
> will do what you want", but it is difficult to recommend the correct option.
>
> Going forward, sending question to a single public list, as Brooke also
> suggests, is best. It is generally considered a good idea to not post to
> two or more, at the same time, with the same email to start threads.
>
> Thanks!
> jen
> Galaxy team
>
>
>> Thanks
>>
>> Kanwar
>>
>>
>>
>> __**_
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>> Galaxy analysis and other features on the public server
>> at usegalaxy.org.  Please keep all replies on the list by
>> using "reply all" in your mail client.  For discussion of
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>> use the Galaxy Development list:
>>
>>
>> http://lists.bx.psu.edu/**listinfo/galaxy-dev<http://lists.bx.psu.edu/listinfo/galaxy-dev>
>>
>> To manage your subscriptions to this and other Galaxy lists,
>> please use the interface at:
>>
>>http://lists.bx.psu.edu/
>>
>>
> --
> Jennifer Jackson
> http://galaxyproject.org
>
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[galaxy-user] SNP analysis in Galaxy

[shamsher jagat]

I posted this question in Dev- list so re-posting to correct list with some
additional information.
I have paired end  sequencing files on which I would like to call SNPs
compared to databases well check sequence variation among samples. I dont
have access to any local galaxy instance. My question are-
1. Is there a way that I can upload these large files to galaxy and analyze
them then delete?
2. Is there a work flow to call SNPs and analyze and annotate SNPS in
Galaxy, If some one know about a work flow summarized  by some one in
addition to  Galaxy list that will be bonus.

Thanks

Kanwar
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[galaxy-user] bcf to vcf

[shamsher jagat]

I wasw wondering if there is any option in Glaxy to convert bcf format to
vcf format?

Thanks

Kanwar
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Re: [galaxy-user] Question about SICER out put

[shamsher jagat]

That is correct, I was able to standardize the work flow, which can be a
starting point for others. I can add to Galaxy shared addition, so that
others may not waste time in looking at what I was searching (at least).

Thanks



On Tue, Aug 7, 2012 at 12:59 PM, Jennifer Jackson  wrote:

> Hi Kanwar,
>
> I found that you also posted this question and another like to the Google
> group for SICER on 7/10 and received some help there:
> http://groups.google.com/**group/sicer-users<http://groups.google.com/group/sicer-users>
>
> Glad that you were able to get the questions resolved. For others reading
> this post or interested in SICER details, follow the documentation links on
> Galaxy's SICER tool form to reach the primary documentation and tool
> author's direct help for how to interpret/understand the various outputs.
>
> There are no community contributed SICER tutorials/pages/workflows (that I
> am aware of, please correct me!), but if developed, I am sure this would be
> a welcomed addition to the "Shared" content on Galaxy Main or
> galaxyproject.org.
>
> Best,
>
> Jen
> Galaxy team
>
>
> On 7/10/12 3:52 PM, shamsher jagat wrote:
>
>> I used SICR to call peaks  and have  following out put files:
>>
>> 1. test.1removed bed
>> 2. control1 removed .bed
>> 3. test w 200 graph
>> 4. test w200 normalized graph
>> 5. test w200-G600 FDR.05 island.bed
>> 6. test w200-G600 FDR .05 island filtered.bed
>> 7. test w200-G600 FDR .05 island filtered normalized.wig
>> 8. test w200-G600 FDR.05 score island
>> 9. test w200-G600 summary  island
>>
>> Which of these files should be used. I think file 5 and 6 are the ones
>> for visualization as well for annotating with genomic regions. I have
>> read the original paper but it is not very clear what these out puts
>> mean. Could some one please guide me what these files mean and what is
>> useful and rest are intermediate files.
>>
>> My second question is authors of SICER has emphasized about teh
>> importance of choosing gap size and window size. gap size they mention
>> 1-3 -5 depending upon the peak distribution, but I see in Galaxy the
>> default is 600 gap size do we need to change it to 1,2- 5 or I am
>> missing something.
>>
>> Any advise please but I did my searching on net.
>>
>> Thanks
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> __**_
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>> Galaxy analysis and other features on the public server
>> at usegalaxy.org.  Please keep all replies on the list by
>> using "reply all" in your mail client.  For discussion of
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>> use the Galaxy Development list:
>>
>>
>> http://lists.bx.psu.edu/**listinfo/galaxy-dev<http://lists.bx.psu.edu/listinfo/galaxy-dev>
>>
>> To manage your subscriptions to this and other Galaxy lists,
>> please use the interface at:
>>
>>http://lists.bx.psu.edu/
>>
>>
> --
> Jennifer Jackson
> http://galaxyproject.org
>
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[galaxy-user] copy number variation detcetion in Glaxay

[shamsher jagat]

Is there any tool/ combination of tools with in galaxy which can detect
CNV. I have 100X paired sequencing data between cancer and normal.

Thanks
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Re: [galaxy-user] genome-wide Bisulfite analyses ... was Re: Infinite TopHat run

[shamsher jagat]

Bjoern,

I interested in trying Bismark under Galaxy. Could you please point me
where I can use it.

Thanks

Kanwar

On Mon, Oct 8, 2012 at 8:08 AM, Björn Grüning <
bjoern.gruen...@pharmazie.uni-freiburg.de> wrote:

> Hi David,
>
> please do not hijack a different thread :)
> If you are analysing Bisulfite data i would recommend to have a look at
> http://www.bioinformatics.babraham.ac.uk/projects/ ... especially at
> bismark.
>
> We have written a wrapper for bismark, its still in testing phase but if
> you like to try it out, you are welcome.
>
> Cheers,
> Bjoern
>
> > Hi, there,
> >
> > I just got two genome-wide Bisulfite sequences from BGI and start to
> > analyze the data.
> >
> > I am trying to use Galaxy; but I find there is no such platform
> > available. Does anybody know where I can find this kind platform at
> > Galaxy or other places.
> >
> > Thanks
> >
> > David
> >
>
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[galaxy-user] sequences for TRAnsfec ids

[shamsher jagat]

This may be  a little different question from usual Galaxy use, I have
alist of Transfec binding matrix ids  -v$1234  and want to extract
bidning sequences corresponding to these ids. Is it possible to extract
such sequences with in Galaxy or anyone aware of an alternative approach
please. I understand that with genomic coordinates I can extract the
sequences in galaxy  but I dont see the genomic coordinates.

Thanks

Kanwar
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[galaxy-user] BWA mapping with index file from history

[shamsher jagat]

I have a Hi-seq Single end data and want to align it to a viral genome and
have fasta file of viral genome. I have created index files out side Galaxy
(I believe I cannot create index file with in Galaxy). The question which I
have is:

There are various index files (v.fasta.amb; v.fasta.pac; v.fasta.rbwt;
v.fasta.rpac; v.fasta.sa) should I be using all the these files as zip file
for index file or one (which one?).


Thanks

Kanwar
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[galaxy-user] combining two fastq files

[shamsher jagat]

Is there an option in galaxy to combine two fastq files?
Thanks

kanwar
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[galaxy-user] Sliding window to get average of a seq reads

[shamsher jagat]

I have a bacterial genome which I divided into bins of 5 bp and counted
reads in each bin. Now I want to use a sliding window of say 100 bp and
count the average. Is there any option in Galaxy that I can do it I have
bed file of data.

Thanks

Kanwar
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[galaxy-user] Windows function not working

[shamsher jagat]

I have been trying to use Region variation > Make window but every time it
returns empty file without any error I have a bed file of custom genome and
has used

chrXX1  10   0.23

Any suggestion please.

Thanks
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[galaxy-user] joining two FASTq files with overlap reads

[shamsher jagat]

I have a data generated from Miseq 2X250 bp these reads are overlap, before
aligning to a my custom bacterial genome, I have to join these two mate
pair Fastq files and then use BWA alignment tool. I am aware of COPE/ FLASH
can be used. I am looking for if there are similar tool or any way I can
join two Fastq files which i can use for alignment. Just to clarify further
with overlapping reads as such BWA is not aligning the reads. I have used
both as mate pair or used only forward reads to align to genome. The idea
is to find SNPs in different samples.

Thanks

Kanwar
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[galaxy-user] Fwd: joining two FASTq files with overlap reads

[shamsher jagat]

Sorry to send  you again and look forward any input abut joining
two overlapping reads Fastq files
Thanks

Kanwar

-- Forwarded message --
From: shamsher jagaut 
Date: Sun, Jan 6, 2013 at 2:24 PM
Subject: joining two FASTq files with overlap reads
To: galaxy-user 


I have a data generated from Miseq 2X250 bp these reads are overlap, before
aligning to a my custom bacterial genome, I have to join these two mate
pair Fastq files and then use BWA alignment tool. I am aware of COPE/ FLASH
can be used. I am looking for if there are similar tool or any way I can
join two Fastq files which i can use for alignment. Just to clarify further
with overlapping reads as such BWA is not aligning the reads. I have used
both as mate pair or used only forward reads to align to genome. The idea
is to find SNPs in different samples.

Thanks

Kanwar
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[galaxy-user] genomic coordinates to Enterz gene ids

[shamsher jagat]

I have a list of around 3000 genomic coordinates of mouse genome and I
would iike to extract gene name Enetrz gene ids Is it possible to extract
this information in galaxy.

Thanks

Kanwar
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[galaxy-user] Bam QC and coverage

[shamsher jagat]

I am looking for a tool to perform QC of Bam file especially following
functions:
1. BAsic information and stat.
2. Coverage across reference features- gene/ transcripts.
Is it possible to do it in Galaxy?
Thanks
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Re: [galaxy-user] Bam QC and coverage

[shamsher jagat]

Thanks for sharing
http://toolshed.g2.bx.psu.edu/repository/view_repository?sort=name&operation=view_or_manage_repository&id=5616f9aed501df32


I was wondering how can I use this tool on tool shed or too shed are
resources only to download and use at their own.
Thanks for your help.


On Thu, Sep 5, 2013 at 12:24 AM, Geert Vandeweyer <
geert.vandewey...@uantwerpen.be> wrote:

>  I've added our BAM-QC/Coverage tool to the toolshed. Search for
> 'coverage_report'
>
>
> http://toolshed.g2.bx.psu.edu/repository/view_repository?sort=name&operation=view_or_manage_repository&id=5616f9aed501df32
>
> It generates a pdf plot similar to the attached one (full exome set, but
> only a few genes in bed file for demo purposes).
>
> Best,
>
> Geert
>
>
>
> On 09/04/2013 09:59 PM, shamsher jagat wrote:
>
> I am looking for a tool to perform QC of Bam file especially following
> functions:
> 1. BAsic information and stat.
> 2. Coverage across reference features- gene/ transcripts.
> Is it possible to do it in Galaxy?
> Thanks
>
>
>
> --
>
> Geert Vandeweyer, Ph.D.
> Department of Medical Genetics
> University of Antwerp
> Prins Boudewijnlaan 43
> 2650 Edegem
> Belgium
> Tel: +32 (0)3 275 97 56
> E-mail: 
> geert.vandewe...@ua.ac.behttp://ua.ac.be/cognitivegeneticshttp://www.linkedin.com/pub/geert-vandeweyer/26/457/726
>
>
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>
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Re: [galaxy-user] Bam QC and coverage

[shamsher jagat]

Joachim , Thanks that is exactly I was looking as Qualimap is exhausting
memory.

Thanks Geert.



On Fri, Sep 6, 2013 at 12:32 AM, Joachim Jacob | VIB |  wrote:

> Hi Shamsher,
>
>
> Another alternative is to use bamqc from the qualimap suite. The wrapper
> you can find at:
> http://toolshed.g2.bx.psu.edu/**view/joachim-jacob/qualimap_**suite<http://toolshed.g2.bx.psu.edu/view/joachim-jacob/qualimap_suite>
>
> You need to install this tool in a local Galaxy, with the qualimap suite
> installed and perl (see README).
>
>
> Cheers,
> Joachim
>
>
>
>  On 09/04/2013 09:59 PM, shamsher jagat wrote:
>>
>
>  I am looking for a tool to perform QC of Bam file especially following
>> functions:
>> 1. BAsic information and stat.
>> 2. Coverage across reference features- gene/ transcripts.
>> Is it possible to do it in Galaxy?
>> Thanks
>>
>
> --
> Joachim Jacob
> Contact details: 
> http://www.bits.vib.be/index.**php/about/80-team<http://www.bits.vib.be/index.php/about/80-team>
>
>
>
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[galaxy-user] using SnpEff and SNPSift in Galaxy

[shamsher jagat]

I have a VCF file and I want to filter it for nonsynonymous/ deletion/
insertion  seq variations. Once I filter this file and compare between
tumor vs normal samples and then annotate such variations.  I believe I can
filter this file using SnpSift and then can annotate with SnpEff, When I
try to use Snsift filter it just says arbitrary expression. Are there rules
how to use expression for a particular filter with in galaxy. If  any one
has used SnpSift in galaxy may share their expertise.

Thanks
Kanwar
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