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biomedicalinformaticsgroup / Sargasso

Sargasso disambiguates mixed-species high-throughput sequencing data.
http://biomedicalinformaticsgroup.github.io/Sargasso/
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Remove --reject-edits option? #35

Closed lweasel closed 8 years ago

lweasel commented 8 years ago

Although I added this with the intention of being able to recreate exactly the original conservative filtering strategy, I'm not sure it's really adding anything above what can be achieved by requiring no mismatches and a full length alignments (i.e. by specifying 0 for --mismatch-threshold and --minmatch-threshold).

Can anyone think of a situation where the CIGAR string output by STAR contains any of the I/D/S/H/P/X operations, where the read would not already be excluded by --mismatch-threshold 0 --minmatch-threshold 0?

s-heron commented 8 years ago

I can't think of a scenario like that in theory & haven't seen one. Certainly not with I/D, I've noticed S doesn't always trigger a mismatch, but then is usually always caught by minmatch. Its possibly hard to say for certain with our data as incidences of I/D/H/P/X are rare if present at all.

lweasel commented 8 years ago

Ok, I think for simplicity's sake I'll remove this then.