Hi,
I am using tophat for the alignment of raw reads to a reference. I have total six samples, and half got around 70% concordant pair alignment rate whereas other half below 40% in the files of align_summary.txt.
I wonder if I need to adjust either the tophat parameters or additional QC processes to try to increase those low alignment rate samples. Because I think all the processes (including mapping and assembly) for each sample should be SAME and thus no bias for the final differential expression. Is it correct?
Thanks!!
Dawn
I am using tophat for the alignment of raw reads to a reference. I have total six samples, and half got around 70% concordant pair alignment rate whereas other half below 40% in the files of align_summary.txt.
I wonder if I need to adjust either the tophat parameters or additional QC processes to try to increase those low alignment rate samples. Because I think all the processes (including mapping and assembly) for each sample should be SAME and thus no bias for the final differential expression. Is it correct?
Thanks!!
Dawn
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