Question: Convert repeat masked out file to bed file format
gravatar for vicky
3.5 years ago by
vicky20 wrote:


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




next-gen • 1.8k views
ADD COMMENTlink modified 3.5 years ago by Devon Ryan81k • written 3.5 years ago by vicky20
gravatar for Devon Ryan
3.5 years ago by
Devon Ryan81k
Freiburg, Germany
Devon Ryan81k wrote:

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 COMMENTlink written 3.5 years ago by Devon Ryan81k

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 REPLYlink written 11 months ago by kk.mahsa70
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