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Forum: Bioinformatics 06-14-2016, 02:41 PM
Replies: 347
Views: 185,353
Posted By cmbetts
Thanks! I thought it was probably something...

Thanks!
I thought it was probably something simple I was leaving out. Adding in the "ordered minlength=1" to the first command preserved the pairs as checked with reformat.sh vpair=TRUE
Forum: Bioinformatics 06-14-2016, 01:08 PM
Replies: 347
Views: 185,353
Posted By cmbetts
Some pairs breaking after multiple steps

I've been doing some multi-step trimming of paired libraries that has been causing a low frequency of pairs breaking, and I'm trying to figure out if there's a way to avoid having this happen.
These...
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