Convert bed12 to GFF

Question

[cmdcolin]

There are several posts online about converting a GFF/GTF to BED12 but is there any way to go the other direction and convert BED12 to GFF?

[agata88]

Converting from BED to SAF/GFF

http://www.raetschlab.org/suppl/gff-tools

Best, Agata

[cmdcolin]

Hi there, I tried out genometools "gt bed_to_gff3 file.bed > out.gff" but it is giving a funny error about "gt bed_to_gff3: error: file "file.bed": line 116470: BED feature has length 0" but the file does not have a line 116470, it is only half that many lines. I dunno where to check for debugging it

[cmdcolin]

I was able to get the BED_to_GFF app that I assume the raetsch lab created at the galaxy server here to work https://galaxy.inf.ethz.ch/ but it is corrupt (the children have same ID as parents) and outputs gtf/gff2 instead of gff3

[agata88]

Could you paste your BED file?

[cmdcolin]

I was checking out this file http://www.igbquickload.org/blueberry/V_corymbosum_Aug_2015/augustus-take6.bed.gz

Answer 1

[ta_awwad]

use bedToGenePred & genePredToGtf UCSC Kent tools: http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/

bedToGenePred.dms  infile.bed  outfile.gpf 

genePredToGtf.dms "file" infile.gpf  outfile.gtf

Answer 2

[alejandrogzi]

Hi! This tool: https://github.com/alejandrogzi/bed2gtf does exactly what you need! It overcomes some limitations of using C binaries.

[alejandrogzi]

Now there is bed2gff, if you want to work only with a gff file!

[onkar]

This tool returns nothing for my file, no errors, no output.

Answer 3

[Juke34]

There is also AGAT that has a convenient bed to gff script (can also produce GTF): https://agat.readthedocs.io/en/latest/tools/agat_convert_bed2gff.html

[onkar]

I tried atat_convert_bed2gff.pl and it worked well.