Has anyone compared ATAC run as PE vs SR? Everyone requests PE but why is that more necessary than, for example, with ChIP or FAIRE?
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Frankly, a lot of people request PE for a lot of applications where it won't help, because they don't know what they're doing and it sounds like more bang for your buck (twice as many reads! /s).
For a good time, take some 2x100 data and see how different your results are if you rerun your pipeline with only read 1, or even with only the first 50 nt of read 1. For vertebrate genomes I find minor differences in alignability between 1x50 and 1x100, and very little difference between 1x100 and 2x100. -
Better mappability (particularly in repeats), better estimation of fragment size? We just did what jwfoley suggested with a PE ChIP library and turns out that fragment estimation was shot at <5M reads using only read 1.Comment
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Thank you! Sorry for lateness, was expecting email notification after responsesComment
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