Question: How convert files .psl to files .bed?
0
gravatar for vaniagarciagonzalez
4.3 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 • 2.2k views
ADD COMMENTlink modified 4.3 years ago by Alex Reynolds30k • written 4.3 years ago by vaniagarciagonzalez0
2
gravatar for Alex Reynolds
4.3 years ago by
Alex Reynolds30k
Seattle, WA USA
Alex Reynolds30k 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 4.3 years ago • written 4.3 years ago by Alex Reynolds30k
0
gravatar for pengchy
7 months ago by
pengchy430
China/Beijing
pengchy430 wrote:

A: Convert BLAT to GFF file?

In that thread, I recommend replacing blat by gmap to perform mapping, gmap could output the alignment result in multiple format, including psl, gff3 and bed. So the conversion between psl and gff would no longer be needed.

ADD COMMENTlink modified 7 months ago • written 7 months ago by pengchy430

GFF and BED are two different formats.

ADD REPLYlink written 7 months ago by Alex Reynolds30k
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