GFF to BED conversion#

It exists many GFF formats and many GTF formats (see here for a complete review) and many tools to perform the conversion. We will try to see in this review the main differences.

Table of Contents#

Test summary#

tool	Comment
AGAT	default RGB color to 255,0,0
PASA	Particular 3rd column that contains a list of names
bedops	each gff feature give one line. Only the 6 first colums are correct
Kent utils	extra coma at the end of 11th and 12th column

The GFF file to convert#

The test file is a GFF3 file:

##gff-version 3
# This is a test sample
scaffold625 maker   gene    337818  343277  .   +   .   ID=CLUHARG00000005458;Name=TUBB3_2
scaffold625 maker   mRNA    337818  343277  .   +   .   ID=CLUHART00000008717;Parent=CLUHARG00000005458
scaffold625 maker   tss 337916  337918  .   +   .   ID=CLUHART00000008717:tss;Parent=CLUHART00000008717
scaffold625 maker   start_codon 337916  337918  .   +   .   ID=CLUHART00000008717:start;Parent=CLUHART00000008717
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   stop_codon  343031  343033  .   +   .   ID=CLUHART00000008717:stop;Parent=CLUHART00000008717
scaffold625 maker   exon    337818  337971  .   +   .   ID=CLUHART00000008717:exon1;Parent=CLUHART00000008717
scaffold625 maker   exon    340733  340841  .   +   .   ID=CLUHART00000008717:exon2;Parent=CLUHART00000008717
scaffold625 maker   exon    341518  341628  .   +   .   ID=CLUHART00000008717:exon3;Parent=CLUHART00000008717
scaffold625 maker   exon    341964  343277  .   +   .   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

AGAT#

AGAT v0.2.2

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

PASA#

PASA pasa-v2.4.1

./PASApipeline/misc_utilities/gff3_file_to_bed.pl test_1.gff > 1_test_transdecoder.bed

#gffTags
scaffold625 337817  343277  ID=CLUHART00000008717;CLUHARG00000005458;TUBB3_2    0   +   337914  343033  0   4   154,109,111,1314    0,2915,3700,4146

bedops#

version: 2.4.37

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    .   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 337915  337918  CLUHART00000008717:start    .   +   maker   start_codon .   ID=CLUHART00000008717:start;Parent=CLUHART00000008717
scaffold625 337915  337918  CLUHART00000008717:tss  .   +   maker   tss .   ID=CLUHART00000008717:tss;Parent=CLUHART00000008717
scaffold625 340732  340841  CLUHART00000008717:cds  .   +   maker   CDS 0   ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
scaffold625 340732  340841  CLUHART00000008717:exon2    .   +   maker   exon    .   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    .   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    .   ID=CLUHART00000008717:exon4;Parent=CLUHART00000008717
scaffold625 343030  343033  CLUHART00000008717:stop .   +   maker   stop_codon  .   ID=CLUHART00000008717:stop;Parent=CLUHART00000008717
scaffold625 343033  343277  CLUHART00000008717:three_prime_utr  .   +   maker   three_prime_UTR .   ID=CLUHART00000008717:three_prime_utr;Parent=CLUHART00000008717

Kent utils#

version from 26-Feb-2020

./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,

The bed format#

Detailed information can be found here: https://genome.ucsc.edu/FAQ/FAQformat.html
Below a description of the different fields:

column	feature type	mandatory	comment
1	chrom	X	The name of the chromosome (e.g. chr3, chrY, chr2_random) or scaffold (e.g. scaffold10671).
2	chromStart	X	The starting position of the feature in the chromosome or scaffold. The first base in a chromosome is numbered 0.
3	chromEnd	X	The ending position of the feature in the chromosome or scaffold. The chromEnd base is not included in the display of the feature. For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases numbered 0-99.
4	name		Defines the name of the BED line. This label is displayed to the left of the BED line in the Genome Browser window when the track is open to full display mode or directly to the left of the item in pack mode.
5	score		A score between 0 and 1000. If the track line useScore attribute is set to 1 for this annotation data set, the score value will determine the level of gray in which this feature is displayed (higher numbers = darker gray).
6	strand		Defines the strand - either '+' or '-'.
7	thickStart		The starting position at which the feature is drawn thickly
8	thickEnd		The ending position at which the feature is drawn thickly
9	itemRgb		An RGB value of the form R,G,B (e.g. 255,0,0). If the track line itemRgb attribute is set to "On", this RBG value will determine the display color of the data contained in this BED line. NOTE: It is recommended that a simple color scheme (eight colors or less) be used with this attribute to avoid overwhelming the color resources of the Genome Browser and your Internet browser.
10	blockCount		The number of blocks (exons) in the BED line.
11	blockSizes		A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
12	blockStarts		A comma-separated list of block starts. All of the blockStart positions should be calculated relative to chromStart. The number of items in this list should correspond to blockCount.

/!\ location BED format is 0-based, half-open [start-1, end), while GFF is 1-based, closed [start, end].