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Question: Rnaseq And Fpkms Per Exon
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gravatar for Slim Sassi
7.6 years ago by
Slim Sassi • 60
Slim Sassi • 60 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.
rna-seq cufflinks • 915 views
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modified 7.6 years ago by Jeremy Goecks • 2.2k • written 7.6 years ago by Slim Sassi • 60
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gravatar for Jeremy Goecks
7.6 years ago by
Jeremy Goecks • 2.2k
Jeremy Goecks • 2.2k 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.
ADD COMMENT • link written 7.6 years ago by Jeremy Goecks • 2.2k
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
ADD REPLY • link written 7.6 years ago by Slim Sassi • 60
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