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/

___________________________________________________________
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/

Reply via email to