[galaxy-user] Fwd: Cufflinks transcript-extract
punjv at yahoo.com
Sun Oct 30 18:58:04 EDT 2011
You should be able to do in Biomart I think fetch seq shoudl also allow you to do the same.
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
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 +
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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