Question: How To Convert Bed Format To Gtf?
4
gravatar for ftp
7.4 years ago by
ftp130
United States
ftp130 wrote:

Hello,

I've seen a lot of posts that convert gtf to bed files. However, i have a bed file that I'm trying to convert to gtf.

Is there any tool that can convert bed->gtf??

Thanks,

gtf bed convert • 16k views
ADD COMMENTlink modified 2.6 years ago by simon.vanheeringen190 • written 7.4 years ago by ftp130
3
gravatar for Alex Reynolds
7.4 years ago by
Alex Reynolds30k
Seattle, WA USA
Alex Reynolds30k wrote:

Depends on the BED data you want to convert to GTF. If your raw data was originally a GTF file converted with BEDOPS gtf2bed, then the lossless conversion result (BED-formatted) contains all the columns you need to rebuild the original data, by simply printing out columns in a different order and setting the correct coordinate index:

$ gtf2bed < foo.gtf | sort-bed - > foo.bed
$ awk '{print $1"\t"$7"\t"$8"\t"($2+1)"\t"$3"\t"$5"\t"$6"\t"$9"\t"(substr($0, index($0,$10)))}' foo.bed > foo_from_gtf2bed.gtf
ADD COMMENTlink modified 7.4 years ago • written 7.4 years ago by Alex Reynolds30k
2
gravatar for Istvan Albert
7.4 years ago by
Istvan Albert ♦♦ 84k
University Park, USA
Istvan Albert ♦♦ 84k wrote:

Changing the coordinate is really simple, just add one to the start coordinate. But the GTF format also needs attributes such as gene_id and transcript_id fields that are not present in the BED format. Therefore you will need a third source of information.

ADD COMMENTlink written 7.4 years ago by Istvan Albert ♦♦ 84k
1
gravatar for simon.vanheeringen
2.6 years ago by
simon.vanheeringen190 wrote:

And another alternative is to combine the UCSC tools bedToGenePred and genePredToGtf.

bedToGenePred in.bed /dev/stdout | genePredToGtf file /dev/stdin out.gtf

You can install these tools with bioconda, or download them here.

ADD COMMENTlink written 2.6 years ago by simon.vanheeringen190
0
gravatar for holgerbrandl
2.6 years ago by
holgerbrandl30
holgerbrandl30 wrote:

Alliteratively you could convert bed to gtf using this kscriptlet:

kscript https://git.io/vbJ4B my.bed > my.gtf
ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by holgerbrandl30
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