Cufflinks transcript-extract

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Cufflinks transcript-extract

dongdong zhaoweiming
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
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Re: 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

Subject: Fwd: [galaxy-user] Cufflinks transcript-extract
---------- Forwarded message ----------From: dongdong zhaoweiming <[hidden email]>Date: Sat, Oct 29, 2011 at 10:38 PMSubject: [galaxy-user] Cufflinks transcript-extractTo: [hidden email]
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
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