Hi,
I have trimmed paired-end reads with Trimmomatic, and some reads are therefore left as only single-end (one pair filtered out entirely). I am using tophat2 to map against a reference genome and my goal is differential gene expression analysis.
My question is if I should include also the single-end reads in the mapping? I am thinking that more reads are better, but are there any drawbacks of including both PE and SE reads?
Thanks!
Jon
I have trimmed paired-end reads with Trimmomatic, and some reads are therefore left as only single-end (one pair filtered out entirely). I am using tophat2 to map against a reference genome and my goal is differential gene expression analysis.
My question is if I should include also the single-end reads in the mapping? I am thinking that more reads are better, but are there any drawbacks of including both PE and SE reads?
Thanks!
Jon
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