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stianlagstad/getSequenceById.sh

Created February 3, 2016 12:23
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Extract specific sequences from a fastq file with this bash oneliner
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getSequenceById.sh
egrep -A 3 '@readid1|readid2|readid3' reads.fastq | sed '/^--$/d'
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-A 3 fetches the matching line and the next three lines.
sed '/^--$/d' will remove the "--" separator lines added automatically by using the -A parameter with egrep.

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