Convert repeat masked out file to bed file format
1
0
Entering edit mode
9.2 years ago
vicky ▴ 30

Hi

Can any one tell me a program or script which I can use to convert the repeat masked.out file to .bed file.

Thanks

next-gen • 4.8k views
ADD COMMENT
4
Entering edit mode
9.2 years ago

You can just use standard command line tools:

awk 'BEGIN{OFS="\t"}{if(NR>3) {if($9=="C"){strand="-"}else{strand="+"};print $5,$6-1,$7,$10,".",strand}}' chrX.fa.out > chrX.bed

You can use column 11 too if you want the family name in the file.

ADD COMMENT
0
Entering edit mode

i have two RepeatMasker .out files (homology_based and de novo identification of repeats). i want to combine these files to obtain a final file but i do not know how do it. following workflow can help me?

  1. converting two RepeatMasker to bed using rmsk2bed

  2. use bedtools intersect

  3. converting final bed to .out (i have no script or program to do it)

ADD REPLY
0
Entering edit mode

Hi,

Why do you increase the start position by using $6-1? Is there a specific reason?

ADD REPLY

Login before adding your answer.

Traffic: 1343 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