I'm just wondering if an experiment run using say 50bp reads and that requires a sequencing depth of 200 million reads to fully assess gene expression, what affect will using 100bp reads have on that sequencing depth? Obviously less sequencing depth would be required, but I was wondering if anyone could give me a rough estimate of how much?
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When using RNA-Seq to study gene expression read length is not a significant factor; what matters is read counts. Whether you align 100bp paired reads or a 50bp single read to a gene they each still only count as one read. It is counts that give you analytical power in expression studies, not how long your alignments are.Originally posted by bob-loblaw View Post -
What kmcarr is saying is correct; counts mean more than the read length in expression analysis. However, a paired end read 2x50bp will be more beneficial than a 100bp single read as it enables the ability to remove PCR duplicates with more precision.Originally posted by kmcarr View PostComment
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