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Old 09-30-2015, 08:21 PM   #43
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

Originally Posted by dkainer View Post
i hadn't noticed the Seal command. Thanks for responding so fast!

So i assume that if I were to input paired-end reads to Seal with a barcodes.fa as the ref, it would try and match the barcodes in both the R1 and R2 reads? Hence the need for skipr1 and skipr2...?
That's correct.

Additionally, would seal let you left trim off the barcode bases from the R1 read?
Yes, it has a flag "ftl" (forcetrimleft) for doing that... "ftl=6" would remove the first 6 bases of all reads. Unfortunately it would do that for both read 1 and read 2. So... if you have reads in 2 files, that's fine; you just process the read1 file with "ftl=6". If they are interleaved it's more complicated - you'd have to split them first (for example, in=reads.fq out=read#.fq). I'll consider adding that the ability to only do all operations on left or right reads... it seems useful.
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