GFF and BED are two different formats.
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Alex Reynolds
How convert files .psl to files .bed?
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
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vaniagarciagonzalez •
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2 answers
You could use psl2bed:
http://bedops.readthedocs.io/en/latest/content/reference/file-management/conversion/psl2bed.html
For example:
$ psl2bed < in.psl > out.bed
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Alex Reynolds
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.
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