SEQanswers (
-   Bioinformatics (
-   -   Strange density plot of log10(fpkm) (

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!

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.

All times are GMT -8. The time now is 10:50 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.