[galaxy-user] Fwd: Cufflinks transcript-extract

[vasu punj]

You should be able to do in Biomart I think fetch seq shoudl also allow you to do the same.
Vasu


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Subject: Fwd: [galaxy-user] Cufflinks transcript-extract

---------- Forwarded message ----------From: dongdong zhaoweiming <zhaoweiming1983 at yahoo.com.cn>Date: Sat, Oct 29, 2011 at 10:38 PMSubject: [galaxy-user] Cufflinks transcript-extractTo: galaxy-user at bx.psu.edu 
Hi,

I use cufflinks to assemble my RNA-Seq reads which produced a GTF file, such as follows:(1)chr1	Cufflinks	transcript	6234876	6235400	1000	+
chr1	Cufflinks	exon	6234876	6235060	1000	+
chr1	Cufflinks	exon	6235239	6235400	1000	+
 
(2)
chr1	Cufflinks	transcript	6230065	6230437	1000 
chr1	Cufflinks	exon	6230065	6230437	1000
 
I want to extract transcrip sequence from the (1) and (2). But fetch sequence could only extract 
genomic sequence, it only fit for transcrit which had one exon,so are there any other tools to extract transcripts which had
 >=2 exons sequence and combine it?
 
Thanks a lot!
weimin zhao ___________________________________________________________The Galaxy User list should be used for the discussion ofGalaxy analysis and other features on the public serverat usegalaxy.org.  Please keep all replies on the list byusing "reply all" in your mail client.  For discussion oflocal Galaxy instances and the Galaxy source code, pleaseuse the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-devTo manage your subscriptions to this and other Galaxy lists,please use the interface at: http://lists.bx.psu.edu/
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