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.

ChenYao

2011/8/9 Jennifer Jackson <jen@bx.psu.edu>

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 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 alignments work well with Cufflinks, but I'm not sure if it
would be possible to use Tophat for my data since miRNA don't have
splice junctions. I've tried without success to parameterize Tophat to
completely avoid assigning splice junctions (by setting the max intron
length to 1). Is there a way I can get the Bowtie alignment to work with
Cufflinks on Galaxy? Or perhaps there's a way I can parametrize Tophat
as to get no splice junctions?

Thanks,

Mete


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