Created
November 7, 2017 16:52
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fastq into 2 files, separating orphans from paired
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| egrep '^@' in.fq | cut -f 1 -d ' ' | sort | uniq -c > in.fq.counts | |
| cat in.fq.counts | egrep " 1 " | ruby -pe 'gsub(/ +1 @/, "")' > in.fq.orphan_ids | |
| cat in.fq.counts | egrep " 2 " | ruby -pe 'gsub(/ +2 @/, "")' > in.fq.paired_ids | |
| then subseq |
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