bedops gff2bed error

Question

[varsha619]

Hello, I am trying to convert a .gff file to bed format using bedops gff2bed tool. Command used - sortBed -i in.gff | gff2bed > out.bed

I get the error - It looks as though you have less than 3 columns. Are you sure your files are tab-delimited? [/apps/bedops/2.4.2/bin/gff2bed] - Error: Please redirect or pipe in GFF-formatted data

Please let me know if there is a way to fix this or use a different tool to convert gff to bed. Thank you as always for your immense help in making my life easier!

Answer 1

[Alex Reynolds]

The gff2bed applies sorting with sort-bed, so presorting with sortBed is unnecessary. Try:

$ gff2bed < in.gff > out.bed

More information is available in the documentation at: http://bedops.readthedocs.io/en/latest/content/reference/file-management/conversion/gff2bed.html

Version 2.4.2 of BEDOPS is very old — nearly three years old! The current version of BEDOPS is v2.4.30. There have been numerous updates to gff2bed and other tools in that time. You should really update, regardless: http://bedops.readthedocs.io/en/latest/content/installation.html

[varsha619]

I see, thank you so much! I will try that out.