How to extract reads which contain specific sequence from fastq file
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!
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WouterDeCoster
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hsu •
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hsu •
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Are you are looking for an exact match of your specific sequence? What have you tried?
What are these sequences, and why not extract them with the grep function?
Use
bbduk.shfrom BBMap suite in filter mode. User guide here. Addliteral=sequence_you_are_looking.If not only looking for exact matches, you can try seqkit grep:
seqkit grep --by-seq --max-mismatch 1 --pattern "ATCGAAG" test.fq