Hello Yan,

To sort a SAM file produced by Bowtie before using it with Cufflinks (a requirement), please see this FAQ and workflow:


http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq#faq2

Best,

Jen
Galaxy team

On 8/14/12 7:33 PM, Yan He wrote:
Hi everyone,

I am working on RNA-seq data. First, I mapped the reads to the reference
transcriptome using bowtie. I found some different reads mapped to the
same gene with different positions. Before running Cufflinks,  I would
like to combine the reads  that mapped to the same gene though with
different positions. Is there a tool in Galaxy can fulfill this purpose?
Any suggestion would be much appreciated. Thanks!

Yan



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