Question: How convert files .psl to files .bed?
0
gravatar for vaniagarciagonzalez
2.3 years ago by
vaniagarciagonzalez0 wrote:

Hello, I need help. I have a file format .psl and I want to convert it to a file format .bed (using the fields 1,2,3,4,5 and 6 of bed) using awk in ubuntu. I have an idea of the commands that can be: awk '{print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6}' file.psl > file.bed

awk .psl .bed • 1.3k views
ADD COMMENTlink modified 2.3 years ago by Alex Reynolds25k • written 2.3 years ago by vaniagarciagonzalez0
1
gravatar for Alex Reynolds
2.3 years ago by
Alex Reynolds25k
Seattle, WA USA
Alex Reynolds25k wrote:

You could use psl2bed:

http://bedops.readthedocs.io/en/latest/content/reference/file-management/conversion/psl2bed.html

For example:

$ psl2bed < in.psl > out.bed
ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by Alex Reynolds25k
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