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Old 01-11-2013, 05:57 AM   #1
Location: Freiburg

Join Date: Oct 2012
Posts: 56
Default 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!

DonDolowy is offline   Reply With Quote
Old 11-05-2013, 09:31 AM   #2
Location: Milwaukee

Join Date: Dec 2011
Posts: 72

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.
gwilymh is offline   Reply With Quote

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