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Convert bed12 to GFF

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?

bed gff bed12
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written by cmdcolin 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

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written by cmdcolin 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

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written by cmdcolin cmdcolin

Could you paste your BED file?

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written by agata88 agata88

3 answers

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
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written by ta_awwad ta_awwad

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

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written by alejandrogzi • alejandrogzi

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

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written by onkar • onkar

nice work on bed2gff...managed to use it! potentially might make some feature requests but otherwise works well

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written by cmdcolin cmdcolin

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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written by Juke34 Juke34

I tried atat_convert_bed2gff.pl and it worked well.

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written by onkar • onkar

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