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
://toolshed.g2.bx.psu.edu/**view/joachim-jacob/qualimap_**suitehttp://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
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
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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Sorry to send you again and look forward any input abut joining
two overlapping reads Fastq files
Thanks
Kanwar
-- Forwarded message --
From: shamsher jagaut kanwar...@gmail.com
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
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
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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Is there an option in galaxy to combine two fastq files?
Thanks
kanwar
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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
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
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 j...@bx.psu.edu 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
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
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
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
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
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
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
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
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
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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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 kanwar...@gmail.com
Date: Wed, Apr 25, 2012 at 7:38 AM
Subject: Question about Samtools filter in Galaxy
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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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
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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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
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
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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Is there any tool (work flow) in galaxy for exome sequence analysis (human/
mouse)
Thanks.
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Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep
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
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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, 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 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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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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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 n...@bx.psu.edu wrote:
On Nov 7, 2011, at 7:11 PM, shamsher jagat wrote:
I uploaded two BAM
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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.
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
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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Galaxy analysis and
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 analysis and other
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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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 tp...@fhcrc.org wrote:
=== Please use Reply All when responding to
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?
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 kanwar...@gmail.comwrote:
Jeremy,
I have been trying to follow the steps in filtering Cufflink out put
files you have described in one
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