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?
Converting from BED to SAF/GFF
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
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
Could you paste your BED file?
I was checking out this file http://www.igbquickload.org/blueberry/V_corymbosum_Aug_2015/augustus-take6.bed.gz
use bedToGenePred & genePredToGtf UCSC Kent tools:
bedToGenePred.dms infile.bed outfile.gpf
genePredToGtf.dms "file" infile.gpf outfile.gtf
Hi! This tool: https://github.com/alejandrogzi/bed2gtf does exactly what you need! It overcomes some limitations of using C binaries.
Now there is bed2gff, if you want to work only with a gff file!
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
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