Convert repeat masked out file to bed file format

Question

[vicky]

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

Answer 1

[Devon Ryan]

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.

[kk.mahsa]

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)

[veritas.ek]

Hi,

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