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skurscheid/get_overrepresented_sequences_from_fastqc.awk

Last active July 1, 2016 04:09
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extract over-represented sequences from FASTQ output file [fastqc_data.txt]
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get_overrepresented_sequences_from_fastqc.awk
awk 'BEGIN{i=0}; {if ($1 == "Filename") {file=$2} else if ($1 ~ /[A|C|T|G]/ && length($1) > 40) {i+=1; print ">",file," ",i,"\n" $1 }}' < fastqc_data.txt
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FASTQC reports over-represented sequences in its fastqc_data.txt output. Sometimes it is necessary to perform a BLAST search of this data. In order to quickly extract these sequences (in this example sequences present more than 40 times), run this awk one-liner to create a FASTA file.

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