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Originally posted by Richard Finney
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They modified the settings to make sure lots of valid alignments are not reported, just like (bowtie -m 1 -v 3). Then they use a better aligner and find more usable reads. Some interesting things about contaminants and quite ambitious to reanalyze all datasets but why not use a better aligner in the first place. -
Well, it's very arguable that Shrimp2 is "better" than BWA/Bowtie2 (whatever that means).
Thank you for the paper though, definitely interesting take on the problem.Comment
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