GFF or BEDfile for Roslin Cg genome RepeatMasker output

[yaaminiv]

How do I convert RepeatMasker output to be something useable with bedtools?

I downloaded the RepeatMasker output from NCBI for the Roslin C. gigas assembly from this link. When I looked at the file, there are a handful of columns that I likely don't need for bedtools intersect.

I tried using the existing RepeatMasker output with intersectBed just to see if it would even accept the file as is. It did not:

I wanted to extract the chr/start/end columns for a BEDfile, but I'm unable to do so!

In the past @kubu4 has provided GFF RepeatMasker output for C. virginica

Is there a way I should modify my RepeatMasker output so I can get a GFF/BEDfile for bedtools?

[kubu4]

Convert to BED file:

tail -n +4 GCF_902806645.1_cgigas_uk_roslin_v1_rm.out | awk 'BEGIN{OFS= "\t"} {print $5, $6, $7}' > GCF_902806645.1_cgigas_uk_roslin_v1_rm.bed

The tail -n +4 skips the first four lines.

EDITED: Hit Answer before I was finished.

[kubu4]

And, I just happened to find this on the RepeatMasker webpage (was only there to get the URL for the software, but happened to notice this):

In addition, we have included a useful python tool (RM2Bed.py) developed by David Ray's lab for manipulating/filtering RM annotation files ( *.out ) and saving output to the BED file format. See the RepeatMasker page for installation details.

That's for versions 4.1.0 and up. We have v4.1.0 installed on Mox if you want to give it a shot.

[yaaminiv]

tail -n +4 GCF_902806645.1_cgigas_uk_roslin_v1_rm.out | awk 'BEGIN{OFS= "\t"} {print $5, $6, $7}' > GCF_902806645.1_cgigas_uk_roslin_v1_rm.bed

That worked. Thanks!

http://owl.fish.washington.edu/halfshell/genomic-databank/cgigas_uk_roslin_v1_rm.te.bed