Hello Alicia,
There are two tools in the main Galaxy Tool Shed
(http://toolshed.g2.bx.psu.edu/) that would likely be helpful. Read the
input requirements for each to decide which is a better fit. Search for
'deseq' to find them:
deseq_and_sam2counts
deseq_hts
To use these tools, a
Sumathy,
It sounds like you're on the right track. To visualize data for a custom build
in Trackster, you need to create a custom build and use that in Trackster:
(1) using the top tabs in Galaxy, go to User -- Custom Builds;
(2) add a new build with the length info as follows:
contig_name
Hi,
I have done exactly the same kind of thing for adenovirus so I can help with
it. In answer to question 1 you do not need to index it will be done for you
when tophat is called. Secondly you should leave the 40 multihits as it is and
post analysis filter out the multihits - this will allow
Hi David,
Thanks!When I tried to run Tophat, it doesn't recognise my FASTA file and
it says History does not include a dataset of the required format /
build. Do you have any thoughts about this?
Now it makes more sense about multihits. Thanks for sharing your
workflow.
With regards
Hi,
You need to run fastq groomer on your rna-seq data. Your reference is fine
as a fasta.
Austin
On Fri, May 6, 2011 at 10:26 AM, puvan...@umn.edu wrote:
Hi David,
Thanks!When I tried to run Tophat, it doesn't recognise my FASTA file and
it says History does not include a dataset of the
Hi Austin
I did all these (grooming and trimming)on rna-seq data and I don't have a
problem with built in genome . I'll try again!
Thanks
Sumathy
On May 6 2011, Austin Paul wrote:
Hi,
You need to run fastq groomer on your rna-seq data. Your reference is fine
as a fasta.
Austin
On
There are many ways. I typically use IGV. It needs a sam file, so I first
convert the bam to sam in galaxy, then download the sam file. In IGV, I
upload the reference and the sam file, then use IGVtools to index the sam
file, then I can visualize the data.
Austin
On Fri, May 6, 2011 at 5:30
Oops. Good to know. Thanks.
Austin
On Fri, May 6, 2011 at 6:02 PM, Sean Davis sdav...@mail.nih.gov wrote:
IGV reads BAM files just fine; no need to convert to SAM.
Sean
On Fri, May 6, 2011 at 8:45 PM, Austin Paul austi...@usc.edu wrote:
There are many ways. I typically use IGV. It
...@mail.nih.gov
Subject: Re: [galaxy-user] RNA seq analysis
To: Austin Paul austi...@usc.edu
Cc: galaxy-user@lists.bx.psu.edu galaxy-user@lists.bx.psu.edu, puvan...@umn.edu
puvan...@umn.edu
Date: Friday, May 6, 2011, 8:02 PM
IGV reads BAM files just fine; no need to convert to SAM.
Sean
On Fri, May 6, 2011
Hi
I may be doing in a wrong way. I clicked trackster and I added the custom
build genome. Since it is a very small genome (~2kb), I considered this as
a single contig. Then I cliked add tracks and added my data file. But I
got a message no data for this contig. Whenever I used built in
Thanks Jim,
Vasu
--- On Fri, 5/6/11, Jim Robinson jrobi...@broadinstitute.org wrote:
From: Jim Robinson jrobi...@broadinstitute.org
Subject: Re: [galaxy-user] RNA seq analysis
To: vasu punj pu...@yahoo.com
Cc: Austin Paul austi...@usc.edu, Sean Davis sdav...@mail.nih.gov,
galaxy-user
,
David
From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu]
Sent: Thursday, April 07, 2011 3:42 PM
To: David K Crossman
Cc: galaxy-user
Subject: Re: [galaxy-user] RNA seq analysis and GTF files
David, can you please share your history with me and I'll take a look (History
Options -- Share/Publish
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,
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