Biostar Beta. Not for public use.
How to extract reads which contain specific sequence from fastq file
0
Entering edit mode
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!

ADD COMMENTlink
2
Entering edit mode

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

ADD REPLYlink
2
Entering edit mode

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

ADD REPLYlink
1
Entering edit mode

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

ADD REPLYlink
0
Entering edit mode

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

ADD REPLYlink

Login before adding your answer.

Similar Posts
Loading Similar Posts
Powered by the version 2.1