How to extract reads which contain specific sequence from fastq file

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4.9 years ago

hsu ▴ 40

Hi, I wanna extract some reads which contain my interest sequence information from fastq file, but these sequence information I interested is in the middle of a read or start of a read. How could I extract these reads?

Thank you!

fastq reads extract • 5.9k views

ADD COMMENT • link updated 4.9 years ago by WouterDeCoster 47k • written 4.9 years ago by hsu ▴ 40

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If not only looking for exact matches, you can try seqkit grep: seqkit grep --by-seq --max-mismatch 1 --pattern "ATCGAAG" test.fq

ADD REPLY • link 4.9 years ago by AK ★ 2.2k

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Use bbduk.sh from BBMap suite in filter mode. User guide here. Add literal=sequence_you_are_looking.

ADD REPLY • link 4.9 years ago by GenoMax 141k

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What are these sequences, and why not extract them with the grep function?

ADD REPLY • link 4.9 years ago by vin.darb ▴ 300

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Are you are looking for an exact match of your specific sequence? What have you tried?

ADD REPLY • link 4.9 years ago by WouterDeCoster 47k

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