Question: Converting GTF file to UCSC-styled bed file
0
gravatar for Javad
19 months ago by
Javad60
Javad60 wrote:

Hello,

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 • 1.3k views
ADD COMMENTlink modified 19 months ago by genecats.ucsc560 • written 19 months ago by Javad60

Hello Javad,

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

ADD REPLYlink written 16 months ago by Vasu330
1
gravatar for cpad0112
19 months ago by
cpad011211k
India
cpad011211k wrote:

Try bedops gtf2bed

ADD COMMENTlink written 19 months ago by cpad011211k
3
gravatar for Pierre Lindenbaum
19 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum120k wrote:

I've written a gff -> 'knownGene file' converter: http://lindenb.github.io/jvarkit/Gff2KnownGene.html , however, I haven't much used it t.

$  curl -s "ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_19/gencode.v19.annotation.gff3.gz" |\
    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 19 months ago by Pierre Lindenbaum120k
2
gravatar for genecats.ucsc
19 months ago by
genecats.ucsc560
genecats.ucsc560 wrote:

There is a UCSC utility for this purpose, gtfToGenePred, which can be downloaded from the directory appropriate to your operating system here:
http://hgdownload.soe.ucsc.edu/admin/exe/

Here is a page (which mostly describes converting in the opposite direction, genePred to gtf), that describes some example usage:
http://genomewiki.ucsc.edu/index.php/Genes_in_gtf_or_gff_format#The_opposite_direction.2C_GTF_to_GenePred

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:

  • genome@soe.ucsc.edu for general questions (public list)
  • genome-www@soe.ucsc.edu for question concerning private data (private list)
  • genome-mirror@soe.ucsc.edu for questions concerning the setup and running of your own UCSC Genome Browser installation

ChrisL from the UCSC Genome Browser

ADD COMMENTlink written 19 months ago by genecats.ucsc560
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1703 users visited in the last hour