I am mapping yeast RNA seq data (ribozero) using Tophat followed by Cufflinks, Cuffcompare, and Cuffdiff to see differential gene expression.
After Cuffdiff, I found that ribosomal RNA reads are all missing, while they are not missing when I used Bowtie2 for mapping. Only difference was that I used Tophat instead of Bowtie2 to integrate at strand information.
I have no idea why ribosomal RNAs are missing, and I am trying to use 'multiread correction' option in Cufflinks if I can fix it.
Can anyone has an idea?
Thanks in advance!