Question: Converting GTF file to UCSC-styled bed file
gravatar for Javad
2.6 years ago by
Javad90 wrote:


I have a gff file and I wnt to convert it to UCSC styled bed file ( tab separated, 12-column). Does any one know a reliable tool that can be used for this conversion?

Thanks in advance

rna-seq next-gen genome • 2.2k views
ADD COMMENTlink modified 2.6 years ago by genecats.ucsc580 • written 2.6 years ago by Javad90

Hello Javad,

Did you sort out how to convert gtf to 12 column Bed file?

ADD REPLYlink written 2.4 years ago by Vasu430
gravatar for cpad0112
2.6 years ago by
cpad011213k wrote:

Try bedops gtf2bed

ADD COMMENTlink written 2.6 years ago by cpad011213k
gravatar for Pierre Lindenbaum
2.6 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum128k wrote:

I've written a gff -> 'knownGene file' converter: , however, I haven't much used it t.

$  curl -s "" |\
    gunzip -c |\
    java -jar dist/gff2kg.jar
1826    ENST00000367917.3   chr1    +   162760522   162782607   162760590   162782210   8   162760522,162762448,162766374,162767591,162769532,162774056,162775183,162782087 162760625,162762652,162766467,162767706,162769727,162774113,162775282,162782607 gene_id=ENSG00000132196.9;transcript_id=ENST00000367917.3;gene_type=protein_coding;gene_status=KNOWN;gene_name=HSD17B7;transcript_type=protein_coding;transcript_name=HSD17B7-201;protein_id=ENSP00000356894.3;havana_gene=OTTHUMG00000034420.6;    ENST00000367917.3
ADD COMMENTlink written 2.6 years ago by Pierre Lindenbaum128k
gravatar for genecats.ucsc
2.6 years ago by
genecats.ucsc580 wrote:

There is a UCSC utility for this purpose, gtfToGenePred, which can be downloaded from the directory appropriate to your operating system here:

Here is a page (which mostly describes converting in the opposite direction, genePred to gtf), that describes some example usage:

If you have any questions or find any bugs in the program, feel free to send a bug report to one of the below mailing lists:

  • for general questions (public list)
  • for question concerning private data (private list)
  • for questions concerning the setup and running of your own UCSC Genome Browser installation

ChrisL from the UCSC Genome Browser

ADD COMMENTlink written 2.6 years ago by genecats.ucsc580
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