Hi Mete,
I am not sure it is the sort problem. I find cufflinks in galaxy is
unstable. I have bam files from Tophat which I can run cufflinks a few days
agao.
But these days when I run cufflinks with these bam files, the error shows.
Strangely, it can work some time. I don't know the reason.
Hi,
Tophat may still be an option for you. You can filter out spliced reads by
filtering column 6 (the CIGAR column) for reads that only map directly (i.e.
c6=='56M' if you have a 56bp paired end read). But I agree with Jen that most
likely it is a sort problem.
Best Wishes,
David.
Hi Mete,
This FAQ has a workflow for sorting a Bowtie (or any) SAM file for
Cufflinks:
http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq#faq2
Thanks!
Jen
Galaxy team
On 8/4/11 10:27 AM, Mete Civelek wrote:
Hi,
I'm trying to get read counts or FPKM values for my miRNA NGS
Hi,
I'm trying to get read counts or FPKM values for my miRNA NGS data on Galaxy. I
have aligned the reads using Bowtie, but it appears that Cufflinks gives an
error when run on the Bowtie alignments (This might have something to do with
Bowtie's BAM file not being sorted). I know that Tophat
4 matches
Mail list logo