Hi Jeremy, I agree that it wouldn't be a good metric to evaluate reads per exon. However, I wanted to use it to document within-transcript coverage bias originating from library construction methods. Thanks for the RSEM suggestion

-Slim

On Apr 8, 2011, at 12:02 PM, Jeremy Goecks wrote:

Hello Slim,

It's not clear to me that reads per exon is a reasonable quantitation metric as many reads are likely to be split across two exons. That said, Cufflinks generates FPKMs by probabilistically assigning reads to transcripts based on both transcript and read characteristics (see http://cufflinks.cbcb.umd.edu/howitworks.html#hqua ), so I don't think there's a way to get Cufflinks to output FPKM by exon. You could try another RNA-seq quantitation package, such as RSEM: http://deweylab.biostat.wisc.edu/rsem/

Good luck, J.

On Apr 8, 2011, at 11:29 AM, Slim Sassi wrote:

...

Hello, Is there a way to get FPKMs per exon? Maybe through modifying the GTF file to trick cufflinks into calculating FPKMs per exon instead of transcript or gene

Thanks

Slim

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

---

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:

http://lists.bx.psu.edu/