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

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