Re: [Useq-users] Question for USeq RNA-seq Analysis Output

[David N. <Dav...@hc...>]

Hello Jeff,

I take it this is from running the OverdispersedRegionScanSeqs?  There's an improved app that replaces this one called DefinedRegionDifferentialSeq.  I'd recommend using this for your subsequent analysis.

Regarding your questions.  Genes with few total reads across the two condition comparison (less than the minimum, default 20) are ignored for all aspects of analysis and reporting in ODRSS (but not in DRDS).  This a gene might be ignored in one analysis but present in another due to that minimum.

-cheers, D

From: Jeff Alexander <jef...@gm...<mailto:jef...@gm...>>
Date: Thu, 6 Sep 2012 15:32:20 -0700
To: USeq <use...@li...<mailto:use...@li...>>
Subject: [Useq-users] Question for USeq RNA-seq Analysis Output

Hello,

I've performed some analysis of RNA-seq data using USeq and I am a bit confused about the output file all.xls.  Can someone tell me what it means if a gene has only gene identifiers and genomic location information but no expression data?  I have assumed that this meant that there were no reads found for this gene in any of the compared datasets.  However, I've recently realized that some of these genes should have reads that map to their coding regions.  For instance, in this experiment I have three conditions that were each compared for differential gene expression.  In some cases, the comparison between Samples 1 and 2 show measured reads in both conditions for a given gene, but comparing Samples 2 and 3 lists this gene as blank.  Any insights would be greatly appreciated.  I've attached an example image of this output, showing genes with no RNA-seq information.

Thank you!

Jeff

Jeffrey Alexander
Graduate Student
Bruneau Laboratory
1650 Owens St.
San Francisco CA, 94122
P: 415-734-2885



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