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Old 09-30-2015, 07:21 PM   #43
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
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Quote:
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.

Quote:
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, reformat.sh 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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