How to extract reads which contain specific sequence from pair-end fastq files
Hi, I wanna extract some reads which contain my interest sequence information from pair-end fastq files,at least 10 bases can be matched, with a maximum of 2 mismatches allowed . How could I extract these reads?
interest sequence like:
GTTTAATTGAGTTGTCATATGTTAATAACGGTAT
CAAATTAACTCAACAGTATACAATTATTGCCATA
thank you！
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cpad0112
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17318598206 •
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17318598206 •
1 answer
You are looking for seqkit grep.
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finswimmer
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For PE, try cutadapt. Your interest sequence is too long (~ 34 nt) and if minimum 10 bases to be matched, rest bases are mismatched and would be higher than 2 mismatches. Requirements are confusing. Are these two sequences are specific (one for R1 and the other for R2) or applicable to both forward and reverse reads?