Dear all,
I am analyzing my 50bp paired-end RNA-seq using the Tophat - Cuffdiff - Cufflinks - cummeRbund pipeline.
I am a little confused on how to interpret the density plot I get from one experiment, where I am comparing ESC, Haploid and Diploid cells.
For the RP sample, I do not see this bimodal distribution, as I see for the other samples.
Is it something I should worry about? I have kind of same shape with another couple of samples from white adipose tissue. My boss flags the normalization as crap as soon as he doesnt see the bimodal distribution, but I am not really sure if it really has to be bimodal. What are your thoughts on this?
The fastqc files pass the fastQC quality controls.
Thanks in advance. Appreciate all inputs!
I am analyzing my 50bp paired-end RNA-seq using the Tophat - Cuffdiff - Cufflinks - cummeRbund pipeline.
I am a little confused on how to interpret the density plot I get from one experiment, where I am comparing ESC, Haploid and Diploid cells.
For the RP sample, I do not see this bimodal distribution, as I see for the other samples.
Is it something I should worry about? I have kind of same shape with another couple of samples from white adipose tissue. My boss flags the normalization as crap as soon as he doesnt see the bimodal distribution, but I am not really sure if it really has to be bimodal. What are your thoughts on this?
The fastqc files pass the fastQC quality controls.
Thanks in advance. Appreciate all inputs!
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