In some examples that I've read for using bwa to analyze paired end data, a fastq for each member of the pair is included (in other words, R1.fastq and R2.fastq). Will bwa handle paired end data that is in a single fastq? The reads are denoted with \1 and \2.
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Originally posted by Protaeus View PostIn some examples that I've read for using bwa to analyze paired end data, a fastq for each member of the pair is included (in other words, R1.fastq and R2.fastq). Will bwa handle paired end data that is in a single fastq? The reads are denoted with \1 and \2.
Code:$ grep -A2 ^@*1 filein.fq > reads_1.fq $ grep -A2 ^@*2 filein.fq > reads_2.fq
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Originally posted by dawe View PostAFAIK no, it won't. You may separate reads into two different files, I guess with
Code:$ grep -A2 ^@*1 filein.fq > reads_1.fq $ grep -A2 ^@*2 filein.fq > reads_2.fq
Code:$ grep -A3 ^"@.*1"$ filein.fq > reads_1.fq $ grep -A3 ^"@.*2"$ filein.fq > reads_2.fq
In a random FASTQ file of ~20m reads I found 511 quality strings which were matched by these grep patterns. An incredibly small fraction to be sure but you need one to screw up your FASTQ file.
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Originally posted by maubp View PostFor the reasons kmcarr gives (and other issues like this), personally I'd use a simple script using Biopython, BioPerl or similar rather than grep.
Nevertheless, I believe grep is much faster than any bioperl/biopython script.
d
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Hi. Just found this post in the GATK forum: http://gatkforums.broadinstitute.org...o-fastq-format
Essentially, you can use BWA with interleaved BAM files containing info from both pairs. I know that was not exactly the question, but it is related, and hopefully will save time for some (as with my case).
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