Strange density plot of log10(fpkm)

[DonDolowy]

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]

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.