Question: How to obtain and compare genomic coordinates from RepeatMasker output?
1
gravatar for gbdias
3.8 years ago by
gbdias80
gbdias80 wrote:

Hello folks!

I want to mask a genome with a particular repeat library using RepeatMasker.

Then I want to cross the coordinates of the repeats with those of gene annotations to find overlaps between them and study associations and stuff.

I'm only starting to consider feasible ways to do that so any input would be great.

Thanks!

ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by gbdias80
2
gravatar for Jon
3.8 years ago by
Jon330
United States - US FS
Jon330 wrote:

Sounds like a job for BedTools.  You should be able to make a GFF from the RepeatMasker output and use bedtools intersect to find overlaps.

ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by Jon330

Thank you very much! I reading BEDTools' documentation and it really seems to be the right tool for this task.

ADD REPLYlink written 3.8 years ago by gbdias80
2
gravatar for SES
3.8 years ago by
SES8.2k
Vancouver, BC
SES8.2k wrote:

The answer by Jon is a good one to get overlaps, and I can tell you how to make the GFF. In the 'util' directory of the RepeatMasker distribution there is a script called 'rmOutToGFF3.pl' that will do the conversion. The usage is pretty simple since it writes to stdout:

perl rmOutToGFF3.pl my_repeatmasker.out > my_repeatmasker.gff
ADD COMMENTlink written 3.8 years ago by SES8.2k

Thank you very much! This will help a lot.

ADD REPLYlink written 3.8 years ago by gbdias80
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