Net file format to Bed
1
0
Entering edit mode
5.0 years ago
int11ap1 ▴ 430

I would like to transform a net file format to a non-redundant bed file format. I know there exists the netToBed executable, but it only gives chromosome - start - end besides of including all parents and children thus being redundant (Since lines overlap).

I would like to have chromosome - start - end - target chromosome in the other species - strand. For that, I used

egrep "^ fill|^net" netfile | awk '{if ($0~/^net/) {chr=$2 ; next} ; print chr"\t"$2"\t"$2+$3"\t"$4"\t"$5}' | sed 's/+//g' > alignment.bed

but this is incorrect as I do not consider children. How would you do that?

Thank you.

bed net alignment • 969 views
ADD COMMENT
0
Entering edit mode
5.0 years ago
ivivek_ngs ★ 5.1k

I do not think this should be able to do what you intend to, since the net file is not a properly tab delimited file. It is having indents describing the parent child relationships. So you can take a look at here or even here and try to perform the tasks.

ADD COMMENT

Login before adding your answer.

Traffic: 1954 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