Question: conversion of GFF3 formate to BED format
0
gravatar for blooming.daisy333
10 months ago by
blooming.daisy33360 wrote:

for finding gene body coverage and other features with RSeQC I need gene annotation file in BED format but my gene annotation file is in GFF3 formate. Can anyone kindly help me how to convert GFF3 format to BED??

many thanks

rna-seq • 894 views
ADD COMMENTlink modified 15 days ago by Kanhu charan Moharana10 • written 10 months ago by blooming.daisy33360

try this : Converting Gff To Bed With Bedtools?

ADD REPLYlink written 10 months ago by vmicrobio240
2
gravatar for finswimmer
10 months ago by
finswimmer11k
Germany
finswimmer11k wrote:

Hello,

you could use ggf2bed from BEDOPS

$ gff2bed < foo.gff3 > foo.bed

fin swimmer

ADD COMMENTlink written 10 months ago by finswimmer11k

Dear finswimmer thank you so much. this suggestion has solved the question and sorry for delayed response. thanks again. but i could not see any sign for accepted/upvote along with you comment to mark it. how to mark?

ADD REPLYlink written 9 months ago by blooming.daisy33360

Hello,

do you use biostars on a mobil device? Than this is sadly at the time not possible. See: Cannot vote in mobil version

fin swimmer

ADD REPLYlink written 9 months ago by finswimmer11k

nope. im using on laptop. it was appearing in my very first few posts that i did marked but now i dont see any sign with comments with any of the post. i could only see upvote signs with replies and nothing else.

ADD REPLYlink modified 9 months ago • written 9 months ago by blooming.daisy33360

Have you changed the Zoom? Which browser are you using?

Try Ctrl+0 to reset the text zoom or Ctrl+-.

fin swimmer

ADD REPLYlink written 9 months ago by finswimmer11k

ohh... thats realy funny. my mistake sorry.. i found it....

ADD REPLYlink written 9 months ago by blooming.daisy33360
0
gravatar for Kanhu charan Moharana
15 days ago by
India
Kanhu charan Moharana10 wrote:

TransDecoder (v5.5.0) has an utility script to convert GFF3 to BEDdetails (12 column) format.

perl TransDecoder-v5.5.0/util/gff3_file_to_bed.pl GFF3 > BED12
ADD COMMENTlink written 15 days ago by Kanhu charan Moharana10
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: 1173 users visited in the last hour