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Old 12-16-2009, 06:06 AM   #2
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543
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Just to clarify - you want to interleave the two paired FASTQ files (F1,F2,F3,... and R1,R2,R3,...) into one file where they alternate (F1,R1,F2,R2,F3,R3,...) but also remove the "/1" and "/2" suffices on the forward and reverse read identifiers to make them the same?

I'd write a script to do this in your language of choice (e.g. Perl perhaps with BioPerl, or Python with Biopython, etc).
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