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
The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at: