conversion of GFF3 formate to BED format

Question

[blooming.daisy333]

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

[vmicrobio]

try this : Converting Gff To Bed With Bedtools?

Answer 1

[finswimmer]

Hello,

you could use gff2bed from BEDOPS

$ gff2bed < foo.gff3 > foo.bed

fin swimmer

[blooming.daisy333]

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?

[finswimmer]

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

[blooming.daisy333]

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.

[finswimmer]

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

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

fin swimmer

[blooming.daisy333]

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

Answer 2

[Juke34]

Here a test of the different solutions made on this gff sample:

##gff-version 3
scaffold625 maker   gene    337818  343277  .   +   .   ID=CLUHARG00000005458;Name=TUBB3_2
scaffold625 maker   mRNA    337818  343277  .   +   .   ID=CLUHART00000008717;Parent=CLUHARG00000005458
scaffold625 maker   CDS 337915  337971  .   +   0   ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
scaffold625 maker   CDS 340733  340841  .   +   0   ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
scaffold625 maker   CDS 341518  341628  .   +   2   ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
scaffold625 maker   CDS 341964  343033  .   +   2   ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
scaffold625 maker   exon    337818  337971  .   +   0   ID=CLUHART00000008717:exon1;Parent=CLUHART00000008717
scaffold625 maker   exon    340733  340841  .   +   0   ID=CLUHART00000008717:exon2;Parent=CLUHART00000008717
scaffold625 maker   exon    341518  341628  .   +   2   ID=CLUHART00000008717:exon3;Parent=CLUHART00000008717
scaffold625 maker   exon    341964  343277  .   +   2   ID=CLUHART00000008717:exon4;Parent=CLUHART00000008717
scaffold625 maker   five_prime_UTR  337818  337914  .   +   .   ID=CLUHART00000008717:five_prime_utr;Parent=CLUHART00000008717
scaffold625 maker   three_prime_UTR 343034  343277  .   +   .   ID=CLUHART00000008717:three_prime_utr;Parent=CLUHART00000008717

• transdecoder (install from conda):

gff3_file_to_bed.pl 1_test.gff 2> 1_test_transdecoder.bed

track name='1_test.gff'
scaffold625 337817  343277  ID=CLUHART00000008717;CLUHARG00000005458;TUBB3_2    0   +   337914  343033  0   4   154,109,111,1314    0,2915,3700,4146

• agat (install from conda):

agat_convert_sp_gff2bed.pl --gff 1_test.gff -o 1_test_agat.bed

scaffold625 337817  343277  CLUHART00000008717  0   +   337914  343033  255,0,0 4   154,109,111,1314    0,2915,3700,4146

• UCSC (donwloaded from their website):

./gff3ToGenePred.dms 1_test.gff temp.genePred ./genePredToBed.dms temp.genePred 1_test_genePred.bed

scaffold625 337817  343277  CLUHART00000008717  0   +   337914  343033  0   4   154,109,111,1314,   0,2915,3700,4146,

• bedops (install from conda):

gff2bed < 1_test.gff > 1_test_bedops.bed

scaffold625 337817  337914  CLUHART00000008717:five_prime_utr   .   +   maker   five_prime_UTR  .   ID=CLUHART00000008717:five_prime_utr;Parent=CLUHART00000008717
scaffold625 337817  337971  CLUHART00000008717:exon1    .   +   maker   exon    0   ID=CLUHART00000008717:exon1;Parent=CLUHART00000008717
scaffold625 337817  343277  CLUHARG00000005458  .   +   maker   gene    .   ID=CLUHARG00000005458;Name=TUBB3_2
scaffold625 337817  343277  CLUHART00000008717  .   +   maker   mRNA    .   ID=CLUHART00000008717;Parent=CLUHARG00000005458
scaffold625 337914  337971  CLUHART00000008717:cds  .   +   maker   CDS 0   ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
scaffold625 340732  340841  CLUHART00000008717:cds  .   +   maker   CDS 0   ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
scaffold625 340732  340841  CLUHART00000008717:exon2    .   +   maker   exon    0   ID=CLUHART00000008717:exon2;Parent=CLUHART00000008717
scaffold625 341517  341628  CLUHART00000008717:cds  .   +   maker   CDS 2   ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
scaffold625 341517  341628  CLUHART00000008717:exon3    .   +   maker   exon    2   ID=CLUHART00000008717:exon3;Parent=CLUHART00000008717
scaffold625 341963  343033  CLUHART00000008717:cds  .   +   maker   CDS 2   ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
scaffold625 341963  343277  CLUHART00000008717:exon4    .   +   maker   exon    2   ID=CLUHART00000008717:exon4;Parent=CLUHART00000008717
scaffold625 343033  343277  CLUHART00000008717:three_prime_utr  .   +   maker   three_prime_UTR .   ID=CLUHART00000008717:three_prime_utr;Parent=CLUHART00000008717

Answer 3

[Kanhu charan Moharana]

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

Answer 4

[alejandrogzi]

There is this new tool called gxf2bed that outperforms most of the current tools. See the tool post here