Sequence extraction

Question

[zhichusun]

Hello, I have a fasta file that contains sequences of different lengths. I want to extract the base sequences greater than 500 and less than 10000bp and regenerate a fasta file. What should I do? Thanks a lot if anyone can help.

Answer 1

[Mensur Dlakic]

One of the ways to do it is with seqkit:

seqkit seq -M 10000 -m 500 file.fas > new_file.fas

[zhichusun]

wa, that's a good way.

Answer 2

[cpad0112]

$ bioawk -c fastx '{ml=500;ML=10000;print (length($seq)>ml && length($seq)<ML)? (">"$name"\n"$seq) :""}' test.fna
$ cutadapt --quiet -m 500 -M 10000 test.fna

Answer 3

[GenoMax]

Using BBMap suite:

reformat.sh in=input.fa out=filterd.fa minlength=500 maxlength=10000