BED file modification
1
0
Entering edit mode
16 months ago
adarsh_pp ▴ 40

Hello,

I have BED file with all the chromosome coordinates.

I need to remove ChrX, ChrY and ChrM from this file.

Please suggest how this can be done.

Thanks

BED NGS Chromosomes • 956 views
ADD COMMENT
1
Entering edit mode

Hello,

The toolkit Bedops is very useful. Here you can see how to extract a specific chromosome with the utility "bedextract".

https://bedops.readthedocs.io/en/latest/content/reference/set-operations/bedextract.html

ADD REPLY
0
Entering edit mode
16 months ago
awk '(!($1=="ChrX" || $1=="ChrY" || $1=="ChrM"))' in.bed
ADD COMMENT

Login before adding your answer.

Traffic: 2291 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