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How to extract reads which contain specific sequence from fastq file

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11 months ago

hsu • 0

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 • 144 views

ADD COMMENT • link • updated 12 months ago WouterDeCoster 39k

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

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genomax 68k

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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

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SMK ♦ 1.3k

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

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darbinator • 180

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

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WouterDeCoster 39k