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Old 03-12-2015, 02:32 PM   #16
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

Originally Posted by vingomez View Post
(1) Is there a flag/command to generate paired reads for mapped reads (e.g. out_ecoli_r1.fq out_ecoli_r2.fq, out_salmonella_r1 out_salmonella_r2.fq.fq)?
Hi Vicente,

I released a new version of BBTools, 34.64. BBSplit now has the ability to output paired reads in dual files using the # symbol. For example: ref=x.fa,y.fa in1=read1.fq in2=read2.fq basename=o%_#.fq

will produce ox_1.fq, ox_2.fq, oy_1.fq, and oy_2.fq

You can use the # symbol for input also, like "in=read#.fq", and it will get expanded into 1 and 2.
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