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  • 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!


  • #2
    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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