Hi Suzanne,
Can you share your history with me and I’ll take a look?
Thanks,
J.
--
Jeremy Goecks
Assistant Professor of Computational Biology
George Washington University
On Mar 24, 2014, at 5:08 PM, Suzanne Gomes suzanneluziago...@gmail.com wrote:
Hello,
I am trying to look
Hi Suzanne,
Thanks for sharing your history. This is a file format issue on our side. We’ll
get it taken care of and let you know when it’s fixed.
Thanks,
J.
--
Jeremy Goecks
Assistant Professor of Computational Biology
George Washington University
On Mar 27, 2014, at 9:27 AM, Jeremy
Indeed, there's another feature I don't fully understand: I have a bgiWig
file that contains reads of only one chromosome. I expected that Circster
would display this one chromosome as one circle, but apparently Circster
always draws a circle where all possible chromosomes of a genome are
1. I tested it using a bigWig and a BED file. Both were loaded nicely in
Circos, but I was surprised to see that the visualization of both files
looked exactly the same, i.e. both file types seemed to be interpreted as
histograms/coverage data. From the Circos plots I've seen in
Is it possible to create a custom build and use it to view a SAM file without
adding the .len and .2bit files in to the Galaxy file system as an
administrator?
Yes, it definitely is.
If so, what am I doing wrong?
This is a Galaxy bug which has been fixed in this commit:
You'll need to set your dataset's database/dbkey to your custom reference
genome before you can visualize it. We have enhancements planned so that this
error doesn't happen in the future.
Best,
J.
On Dec 5, 2013, at 7:56 AM, Jasper Jan Koehorst jasper.koeho...@wur.nl wrote:
I have my own
All reads are in the SAM file; you can filter to remove unmapped reads as
needed.
J.
On Nov 7, 2013, at 5:36 AM, Benjamin Osei-agyeman benjy_o...@yahoo.co.uk
wrote:
Hi
What are the contents of a SAM file after Bowtie has been run? Does it
contain all reads or only those reads mapped
Thanks for the info. However, my problem is that the Tool Version field is
completely empty in my history items (eg. Tophat2, Cuffdiff). I suppose I
can check the dependancies list you described, but it would be important to
know precisely which version was run on any given query.
If
It turns out that your artificial test is a bit too artificial. In order to
display a coverage plot, Trackster converts reads in a BAM to BigWig using a
two step process:
(1) BAM to bedgraph;
(2) bedgraph to bigwig
Your super simple example generates an empty file in step 1 because your single
Hello,
First, I've moved this question from the Galaxy development mailing list to the
Galaxy user mailing list; in the future, please send questions about using
Galaxy to the galaxy-user list.
To answer your question, files larger than 2GB must be uploaded via FTP to
Galaxy. This is
Are you reporting a bug for each failed Cuffdiff run? That's the easiest way
for the Galaxy team to help you out. One thing to keep in mind is that, for
now, spaces are not allowed in condition names. We'll address this problem soon.
Best,
J.
On Oct 22, 2013, at 5:42 AM, Elwood Linney
This sounds an issue with importing workflows. Additional details will help
others provide help:
(1) What version of Galaxy are you using?
(2) What workflow are you trying to import?
(3) What steps have you taken that produce the error that you're seeing?
Thanks,
J.
On Sep 13, 2013, at
Where can I see which version are being used?
You can see both the Galaxy tool version and the Cuffdiff tool version (when
available) by clicking on the 'view details' icon (the 'i' at the bottom of an
expanded dataset). Right now the Cuffdiff version is not displayed, but that
will change
In the past, others have had success using Cummerbund with Galaxy, and there's
even a Cummerbund wrapper in the tool shed:
http://toolshed.g2.bx.psu.edu/view/jjohnson/cummerbund
That said, it appears that replicate information is largely contained in the
read group tracking files, which are
The confidence intervals provided by Cufflinks/Cuffdiff are a good place to
start; any confidence interval that includes 0 should be looked on skeptically.
Good luck,
J.
On Jul 3, 2013, at 2:52 PM, Hoang, Thanh wrote:
Hi all,
I have been working on RNA-seq data analysis using TopHat and
Nothing is wrong with your job, this is a bug in our code that has been
corrected. You'll start seeing the correct parameter values again when we
update our server early next week.
Best,
J.
On May 29, 2013, at 11:05 PM, Du, Jianguang wrote:
Hi All,
After I finshed Tophat alignment
1) My reads are 36nt long. How much should I set for the Minimum length of
reads segments to get the most reliable output with the highest mapping of
splicing junctions?. In my previous run of TopHat, I set it as 18. Can I
reduce it more to get better mapping on splicing junctions?
You'll
I have one more question about the Anchor length. For a RNA-seq read mapped
on the splicing junction under the 0 mismatch condition, if 5 nucleotides of
one end map on one exon, does it mean the rest part of the read must map on
the adjacent exon? What I want to understand is that,
36bp reads will map across splice junctions but at a relatively low rate; you
can try changing segment length to get better mapping, but you'll want to
evaluate the results carefully to ensure that you're getting good results.
Good luck,
J.
On Apr 8, 2013, at 5:45 PM, Du, Jianguang wrote:
Hi
In addition to reducing the the Minimum length of reas segments, do I also
need to reduce Anchor length to get more mapping on splicing junctins?
Definitely worth a try.
Looks like the setting for Anchor length only affects the number of mapped
splicing junctions reported in the .splicing
Cuffmerge does some additional steps that Cuffcompare does not; specifically,
Cuffmerge attempts to remove assembly artifacts:
http://cufflinks.cbcb.umd.edu/manual.html#cuffmerge It's likely that the
(presumed) artifacts removed by Cuffmerge account for the differences that
you're seeing.
The header of the Cuffdiff tool page says it is version 0.0.5
This version is the Galaxy tool wrapper version, not the tool version. (Yes,
this is a usability issue.) You can find the tool version in the dataset's
information panel by clicking on the 'i' icon.
Is there a way, or setting, on
This is likely due to the upgrade from Cufflinks 1.3.x to Cufflinks 2.0.x;
Cufflinks 2.0 introduced a new algorithm for Cuffdiff in particular. You can
read about these changes on the website:
http://cufflinks.cbcb.umd.edu/ (and there's a manuscript describing the changes
as well).
You might
I am dealing with a bacterium which has about 4000 genes. When I tried
Cuffmerge to merge everything with reference annotation, I got a merged file
of only 50 lines. If I left out the reference annotation file, Cuffmerge
returned me a merged file of 4000 lines (which is more reasonable).
Hello,
Apologies for the slow reply. I've moved this thread to the galaxy-user mailing
list because it centers on using Galaxy rather than developing it.
2. deleted the first files, like the first fastq files, but I'm affraid to
have an error messages
Deleting your fastq files after you
My question is, if I need to compare between 5 time points, should I do
comparison pairwise?
No, do them all at once with Cuffdiff:
(a) set 'Perform Replicate Analysis' to 'Yes';
(b) create 5 replicate conditions, one for each time point;
(c) add your replicates for each time point.
Read group info isn't included in the Cuffdiff output right now. I've created a
Trello card to fix this oversight: https://trello.com/c/FdUYdbIn
Best,
J.
On Feb 18, 2013, at 12:32 PM, Johanna Sandgren wrote:
Hi,
I am running cufflinks and cuffdiff using Galaxy. I am however wondering if
Cummerbund is available in the Galaxy toolshed for use in local or cloud
Galaxies:
http://toolshed.g2.bx.psu.edu/view/jjohnson/cummerbund
We haven't put it on our public server yet because there are testing and
compatibility challenges that need to be addressed.
Best,
J.
On Feb 11, 2013, at
In the Add Datasets/Upload Files libraries form, set the option 'Upload option'
to 'Import datasets from your current history' and you'll be able to add
datasets from your history to a library.
Best,
J.
On Jan 27, 2013, at 3:36 AM, Ted Goldstein wrote:
I must be mistaken, but I don't see any
Hello,
Can you share with me (a) the fasta dataset and (b) the form values (e.g. name,
dbkey, etc) you used when you encountered this error?
Thanks,
J.
On Jan 7, 2013, at 10:17 AM, Jennifer Hillman-Jackson wrote:
Repost to Galaxy-user
---
When using Trackster on Galaxy(
This bug has been fixed in our code base; our public server will be fixed when
we update it early next week.
Best,
J.
On Jan 4, 2013, at 5:54 PM, Aaron Stonestrom wrote:
When logged into main trying to create a new shared page under Add new page
in Saved Pages, entering any page title and
Use the replicates option (yes, a bit of a misnomer) and put each Tophat run in
its own group. This will produce a tabular file with FPKM for each group/run.
Best,
J.
On Nov 12, 2012, at 10:05 AM, Vevis, Christis wrote:
Hi,
I got confused while trying to perform Cuffdiff for my RNA
c) if you can create an appropriate input matrix (read counts by exon
or other contig for each sample eg), the Principal Component Analysis
tool might be helpful (library size normalization is one devil that
lies in the detail and it's not quite the same as MDS - see below)
I like starting
Kristis,
This data is available further downstream in an RNA-seq analysis pipeline,
specifically, as output from the Cuffdiff tool. Take a look at the page for
more details:
https://main.g2.bx.psu.edu/rna-seq
Best,
J.
On Nov 9, 2012, at 3:42 AM, Vevis, Christis wrote:
Hi,
I am
I'm able to visualize Cufflinks assembled transcripts in Trackster. Can you
please be more specific about (a) which datasets you're having trouble using
and (b) what errors you're seeing?
Thanks,
J.
On Oct 31, 2012, at 1:10 PM, i b wrote:
Hi all,
can anyone explain me wh how can I visualize
When you say large history, is there a size limit that I should be aware of,
or will it handle anything that my quota can accept?
It will handle anything your quota can accept.
Best,
J.
___
The Galaxy User list should be used for the
be identical to the history that I was having problems with yesterday. I can
share with you the original history once the jobs have finished running (but
it might take a while).
Thanks,
Dave
On Wed, Oct 17, 2012 at 10:35 PM, Jeremy Goecks jeremy.goe...@emory.edu
wrote:
Dave,
There's
You'll need to update the tool_data_table_conf.xml file in your Galaxy home
directory.
If you haven't made changes to the file, you can copy
tool_data_table_conf.xml.sample to tool_data_table_conf.xml If you have made
changes, add these entries to the file:
--
table name=bowtie2_indexes
Dave,
There's likely something problematic about your history that causing problems.
Can you share with me the history that's generating the error? To do so, from
the history options menu -- Share/Publish -- Share with a User -- my email
address
Thanks,
J.
On Oct 17, 2012, at 6:58 PM,
Hi El,
1) what do these numbers represent?
FPKM values for sample 1 and 2. Cufflinks documentation is the place to get
definitions for all columns:
http://cufflinks.cbcb.umd.edu/manual.html#gene_exp_diff
2) If in the value column where I expect a higher number has a value of
10 or less
Sarah,
I can't reproduce this behavior on a local instance or on our public server.
This raises a couple questions:
Are you using the most recent version of Galaxy?
Can you reproduce this behavior on our public server (usegalaxy.org)?
Thanks,
J.
On Jul 31, 2012, at 8:13 AM, Sarah Maman
There is an excellent article on how to do differential gene/transcript
expression with Tophat and Cufflinks here:
http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html
This article will answer the questions you've posed below and provides numerous
figures that will help you
in Trackster.
Best,
J.
On Jul 13, 2012, at 5:34 PM, Nancy Au Yeung wrote:
On Fri, Jul 13, 2012 at 2:29 PM, Jeremy Goecks jeremy.goe...@emory.edu
wrote:
Hi Nancy,
Can you share the history with the problematic dataset(s) with me and I can
take a look? Please share the history with me
Hi Nancy,
Can you share the history with the problematic dataset(s) with me and I can
take a look? Please share the history with me using my email address:
jeremy.goe...@emory.edu
Best,
J.
On Jul 12, 2012, at 9:07 PM, Nancy Au Yeung wrote:
Hi,
I saw another post regarding trackster error
down the
host computer).
Additional suggestions most welcome…
Todd
On Apr 17, 2012, at 6:33 PM, Jeremy Goecks wrote:
Hi Todd,
[Not sure if this is better suited to galaxy-dev or -user, so I'm sending
to both].
galaxy-user is most appropriate for this question because
I am wondering if these non-coding reads will be included when cufflinks
calculates transcript/gene expression.
Reads will only be included if they map to assembled/known transcripts.
And another question is: how to know the number of reads mapped to a certain
exon?
This isn't possible
Jeremy, do you have a workflow to estimate what percent of the reads
are mapping to unknown expressed regions?
Here's a simple approach assuming mapped reads are in BAM format:
BAM -- SAM
SAM -- Interval
Intersect reads as interval with known annotation not allowing for any overlap.
Best,
Hi Todd,
[Not sure if this is better suited to galaxy-dev or -user, so I'm sending
to both].
galaxy-user is most appropriate for this question because it related to usage
of Galaxy; galaxy-dev is for local installation and tool development questions.
My question is - can I create a
Scott,
Your information is incorrect. The Galaxy Community Conference (
http://wiki.g2.bx.psu.edu/Events/GCC2012 ) will have something for everyone who
is working with Galaxy, from sys admins to tool developers to core staff to end
users/biologists.
Our program is still in flux, and we
Mackenzie,
We've fixed this issue in our code base and it should be fixed on our server in
the next day or two.
Best,
J.
On Mar 22, 2012, at 3:35 PM, Mackenzie Gavery wrote:
Hi,
I am working with some saved visualizations, and finding that the color
settings are not working today.
Nick,
I apologize if this is covered in documentation or help threads. searched
and it seemed it was not. I have several illumina rna-seq data sets that
should be directional. It seems the directionality is very good, based on
the visualization. First question is; in the visualization
Bomba,
I'm not familiar enough with bacterial/prokaryotic transcriptomes to suggest a
possible workflow. You might try the standard
Tophat-Cufflinks-Cuffcompare/merge-Cuffdiff workflow and see whether you get
meaningful results; Tophat runs Bowtie internally, so there's no reason to run
The problem ended being the use of Perform Bias Correction(-b) and a
GTF file with no Database/Build associated. Looking at cuffdiff
wrapper I found, if a FASTA reference is not selected from the
history, the FASTA reference of the GTF file associated build is used.
If there is not build
1. It seems that it is better to run everything up to cuffdiff, but does
cuffdiff allow multiple sample comparison because I read somewhere that even
for multi-samples it still compare tham pairwisely?
Cuffdiff supports replicate analysis.
In a sense, because I want to do clustering which
Victor,
I got the normalized values (FPKM) from cufflinks. And I want to get relative
reads counts. How can I do that?
It's not clear to me what you're looking for. FPKM is a normalized read count
metric where the F stands for fragment, which is a single read (or half of a
paired read).
. Could you please tell me how
to get those?
Thank you very much!
Victor
From: Jeremy Goecks [jeremy.goe...@emory.edu]
Sent: Thursday, February 09, 2012 4:00 AM
To: Li, Jilong (MU-Student)
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] How to get reads
Peera,
Turning off bias correction can significantly shorten Cufflinks runtime.
If you still encounter this error, you'll want to use a local or cloud instance
of Galaxy:
https://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy
http://wiki.g2.bx.psu.edu/Admin/Cloud
Good luck,
J.
On Jan 30,
Noa,
This is one thing I would like help with- is it worth simply reducing to
nothing the max intron size? What is accepted consensus when using tophat on
bacterial genomes?
I'm not sure that folks on this list have much experience with bacterial
transcriptome analysis. You might try
Erin,
This was due to a temporary issue that has been fixed. However, you'll need to
copy the problematic datasets and use the new copy for visualization. To copy
datasets, use History Options -- Copy Datasets; you can select the source
history as your target history to copy datasets within a
Wei,
The pileup tool will help you find SNPs in your data; you'll want to read the
documentation to understand how best to use it for your needs. You can also try
the Unified Genotyper on our test server ( http://test.g2.bx.psu.edu/ ), but
it's in alpha/beta status and we aren't providing any
Efthymois,
You'll want to run Galaxy as a daemon process. Run
% sh run.sh --help
to get more information on running Galaxy as a daemon.
Also, please direct questions about running/configuring a local Galaxy instance
to galaxy-dev (cc'd) rather than galaxy-user, which is for tool and analysis
Noa,
Using your FASTA in Tophat and Cufflinks is the correct approach. You don't
need to provide an annotation file in Cufflinks, and you can also avoid using
your FASTA in Cufflinks by not using bias correction.
If you're still having problems, the issue is likely your parameter choices in
Baohua and Jane,
As David noted, there is a Trinity wrapper for Galaxy, it works, and Trinity is
great.
However, Trinity is not enabled/installed on our public server (main.g2) or on
Galaxy cloud instances (Amazon) right now. You'll need a little programming
expertise to set up Trinity
Rebecca,
You should be able to use a custom genome with this tool by selecting History
from the Source for Genomic Data parameter.
The bug you're describing has, to the best of my knowledge, been fixed in
Galaxy and should not be present anymore. On which Galaxy instance are you
seeing this
Thanks for your help. I'm mapping reads from one organism to a related but
different organism, so some of the parameters I'd like to adjust are to relax
mapping stringency -specifically:
-n 3 (allow 3 mismatches in seed)
-e 250 (allow cummulative phred score of 250 [or some other value
Jeremy,
My apologies if this has been covered before but I am using Galaxy Main and
wonder if, when running TopHat, you can modify the mapping parameters used by
Bowtie?
Not all Bowtie parameters can be modified when running Tophat. Which parameters
are you looking to modify and why?
It
There is currently no way to do this but it would definitely be a useful
option to have. I've opened a ticket that you can follow and/or comment on if
you're interested:
https://bitbucket.org/galaxy/galaxy-central/issue/680/preserve-dataset-names-when-exporting
I forgot to mention that
Also another question about permissions. If I create a Galaxy page and share
that with limited users then it appears that the datasets are all public via
a URL is that correct?
Yes, all datasets are public via URL by default in Galaxy, and a Galaxy Page
makes it easy to find this URL.
?
On Thu, Oct 13, 2011 at 12:12 PM, Jeremy Goecks jeremy.goe...@emory.edu
wrote:
Chandu,
There are two problems:
(1) you mapped your reads to AgamP3, but the dbkeys for all of your Cufflinks
datasets is anoGam1. This should not have happened automatically with Galaxy,
but I'm
Cecilia,
Are you trying to use the Public Galaxy or a local install? There
are several assemblers with Galaxy Wrappers on the Galaxy
ToolShed (e.g. Roche Newbler, and MIRA 3) which you could
add to your own local Galaxy if you have one.
There are wrappers for ABySS as well. These assemblers
From: Jeremy Goecks jeremy.goe...@emory.edu
To: Richard Mark White whit...@yahoo.com
Cc: galaxy-user@lists.bx.psu.edu galaxy-user@lists.bx.psu.edu
Sent: Sunday, August 28, 2011 2:18 PM
Subject: Re: [galaxy-user] rna-seq mutation detection
Rich,
Given that you're analyzing your RNA-seq data
=== Please use Reply All when responding to this email! ===
Rich,
Given that you're analyzing your RNA-seq data using Galaxy, I'd guess that
you're using Tophat to map your reads onto on reference genome. If this is the
case, then you can use the BAM files produced by Tophat to generate
=== Please use Reply All when responding to this email! ===
David,
Quartile normalization is explained in the Cufflinks manual:
http://cufflinks.cbcb.umd.edu/manual.html --
With this option, Cufflinks normalizes by the upper quartile of the number of
fragments mapping to individual loci
Crystal,
If you provide a gene annotation to Cufflinks, the transcripts
produced will match those in the annotation exactly. If you assemble
without a gene annotation, the transcripts produced will match the
reference in some cases, but, in others, will not match the reference
due to
Yao,
It's difficult to tell what's wrong without seeing your analysis. However, you
may want to use the reference annotation during the Cufflinks phase to either
estimate isoform expression or guide assembly (this option will appear on our
public server soon). Read the Cufflinks documentation
Carol,
My question is, if I use the public Galaxy server interface to TopHat and
Cufflinks, is there any access to cuffmerge?
No, Cuffmerge is not available in Galaxy.
Also, I'm trying to understand the difference between using cuffmerge and
then using cuffcompare (without a reference
Jiannong,
Hans is on right track. You can indeed visualize your data using Trackster,
Galaxy's genome browser; Trackster is available via the Visualization tab.
Here are the steps needed to visualize your dataset:
(1) Use the [FASTA Manipulation -- Compute Sequence length] tool to compute
Kurinji,
1. when I look at my differentially expressed transcripts file (generated
using ensembl hg19 as a reference with chr added on to obtain results with
ensembl gene names) and search for specific genes that I am interested in I
can not find them in my cuffdiff output file - even
Hello Kurinji,
I was at your USC Galaxy seminar last week, which I found very helpful -
thank you!
Glad to hear that you found the workshop helpful. As a reminder, please email
questions about using Galaxy and its tools to the galaxy-user mailing list
(which I've cc'd). You may get quicker
Thanks for the reply. I tried to use the script provided on a previous galaxy
thread for adding the chr on to the gtf file on the mac terminal but I keep
getting this error -
awk: can't open file ensembl.gtf
source line number 1
I am very new to using the terminal so please let me
Hello Wen,
It's not necessary to send multiple emails to the mailing list; we track
incoming emails to ensure that we respond to all of them.
Your FPKM values do look high, but keep in mind that coverage is only part of
the FPKM calculation; it's also dependent on transcript length and the
Stephen,
This is a formatting issue with your input file; it needs to be tab-delimited
but it's not currently. You'll need to:
(a) convert spaces to tabs using the Convert delimiters to Tabs tool;
(b) click on the pencil icon and set the data type to BED.
Best,
J.
On Jun 21, 2011, at 8:45 AM,
Felix,
You seem to be providing the correct inputs to Cuffdiff and it appears to be
producing valid output. More information about setting parameter values and
interpreting Cuffdiff can be found in manual:
http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff
Good luck,
J.
On Jun 16, 2011, at
John,
My best guess is that you are using bias correction but do not have the needed
reference genome(s) for the builds that you want to use. See this page for
instructions about setting up HTS tools; in particular, you'll need to set up
the sam_fa_indices.loc file:
Edge,
Please send questions like this to the galaxy-user mailing list, where many
people see your email and can help you and/or benefit from it. I've cc'd the
list for this reply.
The thread you linked to is out of date. To get sequences for the features in a
GTF file, you can use the
Jagat,
First, a couple housekeeping issues:
(a) the questions you're asking are better suited to the galaxy-user list
(questions about using Galaxy and performing analyses) rather than galaxy-dev
(questions about installing Galaxy locally and tool development), so I've moved
this thread to
(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
. But I got a
message no data for this contig. Whenever I used built in genomes I did not
have any problem. I guess I am doing something wrong here.
Sumathy
On May 6 2011, Jeremy Goecks wrote:
Sumathy,
What kind of problems are you having with Trackster?
J
tracking file. I tried but I dont see track browser unless i
convert to GTF file format. Further if you can point me how to get the slider
window function as shown in snap shot that will be great. Good work Jeremy!
Thanks.
Vasu
--- On Sun, 4/17/11, Jeremy Goecks jeremy.goe
a old fashion way but my boss is a big fan of using IGB
to see expression file(wig or sgr file) and do some analysis. THanks a lot!
BEst
Ying
Quoting Jeremy Goecks jeremy.goe...@emory.edu:
Hi all,
Ann is correct - Tophat does not produce .wig files when run anymore.
However, it's
?
Thanks.
Vasu
--- On Mon, 4/11/11, Jeremy Goecks jeremy.goe...@emory.edu wrote:
From: Jeremy Goecks jeremy.goe...@emory.edu
Subject: Re: [galaxy-user] downstream analysis of cuffdiff out put
To: shamsher jagat kanwar...@gmail.com
Cc: galaxy-user galaxy-user@lists.bx.psu.edu
Date: Monday, April 11, 2011
Now why does a tool search on the public Galaxy instance for GC
not suggest this tool?
Name: geecee
Description: Calculates fractional GC content of nucleic acid sequences
Does this mean the description isn't searched? It would seem like
a sensible idea to me to include that...
On Thu, Mar 10, 2011 at 7:55 AM, Jeremy Goecks jeremy.goe...@emory.edu
wrote:
Jagat,
Just like any mRNA-seq experiment to achieve following objectives:
1. Reconstruct all transcripts of a particular gene and corresponding
Cuffdiff significantly expressed transcripts as called
appreciated.
Thanks,
David
-Original Message-
From: galaxy-user-boun...@lists.bx.psu.edu [mailto:galaxy-user-boun...@lists.bx.psu.edu
] On Behalf Of Jeremy Goecks
Sent: Friday, April 01, 2011 8:47 AM
To: ssa...@ccib.mgh.harvard.edu
Cc: galaxy-user
Subject: Re: [galaxy-user] RNA seq
On Mar 31, 2011, at 12:30 PM, ssa...@ccib.mgh.harvard.edu
ssa...@ccib.mgh.harvard.edu wrote:
Hi Jeremy,
I used your exercise to perform an RNA-seq analysis. First I encountered a
problem where the gene IDs were missing from the results. Jen from the Galaxy
team suggested this:
Yes,
Cristian,
Please share your history with me (History Options -- Share/Publish -- Share
with User -- my email) and I'll take a look.
Thanks,
J.
On Mar 30, 2011, at 10:48 AM, Cristian Rojas wrote:
Hi everybody, I am trying to analyze the differential expression between two
RNAseq samples.
original
De: Jeremy Goecks jeremy.goe...@emory.edu
Para: Cristian Rojas cristianroja...@yahoo.com.ar
CC: galaxy-user@lists.bx.psu.edu
Enviado: miércoles, 30 de marzo, 2011 12:53:50
Asunto: Re: [galaxy-user] Trouble with RNAseq analysis
Cristian,
The contig names in your GTF file
I tried agaian and the same problem. I tuned off the bias correction
but
mantained the GFT file. May be this is the problem? I didnt find
your history.
Thanks
Look for the history I've shared in History Options -- Histories
Shared with Me. As requested, if you're still having problems,
Karen,
Sorry for the slow reply. There are no immediate plans to add either
BED-to-GFF3 or GTF-to-GFF3 converters to Galaxy main or the Galaxy codebase.
However, if you're working with your own Galaxy, you might encourage the Rätsch
lab to contribute their tools to the Galaxy Tool Shed
Jagat,
Please send queries such as these to the galaxy-user mailing list (cc'd); there
are many users on the list who can contribute to this discussion, and there are
many additional users that will benefit from this discussion.
I was wondering if you can point me to a documentation or URL to
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