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-   -   Strange density plot of log10(fpkm) (http://seqanswers.com/forums/showthread.php?t=26418)

DonDolowy 01-11-2013 05:57 AM

Strange density plot of log10(fpkm)
 
Dear all,

I am analyzing my 50bp paired-end RNA-seq using the Tophat - Cuffdiff - Cufflinks - cummeRbund pipeline.
I seem to get very nice plots with most of my data, but for one specific tissue I get a strange density plot for the KO sample with just one peak (like a shoulder) instead of the usual shape I get being the case for Ctrl.

Do you know what is causing this distribution and is it something I would have to worry about?

The fastqc files pass the fastQC quality control.

Thanks in advance. Appreciate all inputs!

http://imageshack.us/scaled/landing/...30111at348.png

gwilymh 11-05-2013 09:31 AM

The KO and the Ctrl graphs look normal to me. The slight change in the peak shapes could be a result of slightly different levels of gene expression between the two samples.


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