Question: Convert bed12 to GFF
0
gravatar for cmdcolin
12 months ago by
cmdcolin700
United States
cmdcolin700 wrote:

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?

bed12 gff bed • 557 views
ADD COMMENTlink written 12 months ago by cmdcolin700
1

Converting from BED to SAF/GFF

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

Best, Agata

ADD REPLYlink written 12 months ago by agata88630

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

ADD REPLYlink written 12 months ago by cmdcolin700

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

ADD REPLYlink modified 12 months ago • written 12 months ago by cmdcolin700

Could you paste your BED file?

ADD REPLYlink written 12 months ago by agata88630

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

ADD REPLYlink written 12 months ago by cmdcolin700
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