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Old 02-05-2015, 10:33 AM   #8
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Location: California

Join Date: Aug 2010
Posts: 3

I would highly recommend this blog from CoreGenomics which tries to address this issue using the data published by the SEQC group last year:

Bottom line is that many independent groups have come to the same conclusion: 10M to 20M single-end 50 bp reads (from libraries made with polyA mRNA preps) will give gene-level expression values that are better than an AFFY array.

These days, what with the lower price of sequencing etc., I always try to default to 25M paired-end 2x75 bp reads. This data will persist for a long time and can be used by lots of different pipelines to do more advanced analysis of splicing, fusions, and novel transcript discovery than can be done with 50 bp SE reads alone.
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