Remove A List of Sequences from the MSA File
1
0
Entering edit mode
5 months ago
Tastulek • 0

Hello Everyone,

I have an MSA file containing hundreds of sequences aligned by BWA. Now I would like to remove a list of sequences from the MSA file, is there a quick way to do this? or Could the MSA file be split into two?!

I would appreciate your response!

BAMtools SAMtools Multiple BWA BCFtools Alignment Sequence • 375 views
ADD COMMENT
2
Entering edit mode
5 months ago
atorreso ▴ 120

You can prepare a list with the sequences you want to keep (so the reverse of the sequences you want to remove) and use seqtk. As explained in their github (https://github.com/lh3/seqtk):

 seqtk subseq in.fq name.lst > out.fq
ADD COMMENT
0
Entering edit mode

atorreso Thank you so much!

ADD REPLY

Login before adding your answer.

Traffic: 2200 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6