You should be able to do in Biomart I think fetch seq shoudl also allow you to
do the same.
Vasu
Subject: Fwd: [galaxy-user] Cufflinks transcript-extract
-- Forwarded message --From: dongdong zhaoweiming
zhaoweiming1...@yahoo.com.cnDate: Sat,
Jen,
I ran the flow as you suggested, but got following error message, Do You hav
eany suggestion? I added 0 and flips the columns: Here is the few lines of
input file:
chr1
12137
12336
61R33AAXX100706:1:79:7707:9270
0
-
chr1
31542
31741
61R33AAXX100706:1:37:11341:10600
1
-
chr1
39921
If using Ensembl make sure it is properly formatted.
Vasu
--- On Tue, 8/30/11, Peng, Tao tp...@fhcrc.org wrote:
From: Peng, Tao tp...@fhcrc.org
Subject: [galaxy-user] annotation file for cufflinks
To: Jennifer Jackson j...@bx.psu.edu, galaxy-user
galaxy-user@lists.bx.psu.edu
Date: Tuesday,
UCSC should work fine.
Vasu
--- On Tue, 8/30/11, Peng, Tao tp...@fhcrc.org wrote:
From: Peng, Tao tp...@fhcrc.org
Subject: RE: [galaxy-user] annotation file for cufflinks
To: vasu punj pu...@yahoo.com, Jennifer Jackson j...@bx.psu.edu,
galaxy-user galaxy-user@lists.bx.psu.edu
Date: Tuesday
IGV should allow you to do this but not sure about trackbrowser in Galaxy.
Vasu
--- On Wed, 8/3/11, Jiannong Xu j...@nmsu.edu wrote:
From: Jiannong Xu j...@nmsu.edu
Subject: [galaxy-user] visualization
To: galaxy-user@lists.bx.psu.edu galaxy-user@lists.bx.psu.edu
Date: Wednesday, August 3,
Jen/ Jeremy/ Galaxy team,
Is there any plan of implementing gene fusion version of TopHat in Galaxy
perhaps in next few months or so? Alternatively, if some one has used with gene
fusion using TopHat in Galaxy frame work please share.
Thanks.
Vasu
It appear that you are talking about RNA-seq data analysis. If so please read a
tutorial posted by Jeremy to get an idea how the work flow has to be used. I am
sure folks would also like to know what error you are getting.
--- On Thu, 7/28/11, archana bhardwaj archana2...@gmail.com wrote:
your pid must also be empty.
I think:
-s seq_dir Causes cuffcompare to look into for fasta files with the
underlying genomic sequences (one file per contig) against which your reads
were aligned for some optional classification functions. For example, Cufflinks
transcripts consisting mostly of
Will submit to Galaxy my additions.
Thanks
Vasu
--- On Wed, 7/6/11, Jeremy Goecks jeremy.goe...@emory.edu wrote:
From: Jeremy Goecks jeremy.goe...@emory.edu
Subject: Re: [galaxy-user] Looking for new transcripts with cufflinks
To: vasu punj pu...@yahoo.com
Cc: GavinOliver gavin.oli
One question related to this If I am intrested in annotated genes/transcripts,
what change I may have to make in command line while runnig Cufflinks so that
it will give both unknown as well as known transcrpts and genes?
Thanks
--- On Mon, 7/4/11, David Matthews d.a.matth...@bristol.ac.uk
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
I have a question on using Bowtie vs TopHat. I do understand that TopHat call
Bowtie and if followed by cufflink and cuffdiff will give transcript
differential expression etc. and most of reads will be mapped to exons across
junctions. Anyone has tried using Bowtie with same reads and
If it is ChIP-motif you may like to consider
http://motif.bmi.ohio-state.edu/ChIPMotifs/
There are several others but this is my favorite.
Vasu Punj
--- On Fri, 2/25/11, Christopher Futtner christopher.futt...@duke.edu wrote:
From: Christopher Futtner christopher.futt...@duke.edu
Subject
I have used IGV with the Bam file and one ha sto generate index file which can
be done in IGV, it work well. Gbrowser should also be OK. I think new version
of IGV provide lot more features than previous one
Vasu.
--- On Fri, 2/18/11, Peter biopyt...@maubp.freeserve.co.uk wrote:
From: Peter
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