Some quick notes on common file formats used in the bioinformatic world I am now part of.
GFFv2
Apparently there are 3 different versions of GFF from 2 different sources. GFFv2 and GFFv3 are the most interesting currently.
Name
General Feature Format (v1,v2)
Format
Nine required fields that must be tab-separated.
- seqname - The name of the sequence. Must be a chromosome or scaffold.
- source - The program or database that generated this feature.
- feature - The name of this type of feature. Some examples of standard feature types are “CDS”, “start_codon”, “stop_codon”, and “exon”.
- start - The starting position of the feature in the sequence. The first base is numbered 1.
- end - The ending position of the feature (inclusive).
- score - A score between 0 and 1000. If no score, then ‘.’ is used
- strand - Valid entries include ‘+’, ‘-’, or ‘.’ (for don’t know/don’t care).
- frame - If the feature is a coding exon, frame should be a number between 0-2 that represents the reading frame of the first base. If the feature is not a coding exon, the value should be ‘.’. Field should be called “Phase”
- attribute - not-well defined field with tag value ; structure
Application Support
Source
GFF v1 & GFF v2 come from The Sanger Institute
GFFv3
Name
Generic Feature Format (v3)
Format
9 fields separated by tab characters
Application Support
- SnpEff - for new genome creation
Source
GFF v3 comes from The Sequence Ontology Project
Example
0 ##gff-version 3
1 ##sequence-region ctg123 1 1497228
2 ctg123 . gene 1000 9000 . + . ID=gene00001;Name=EDEN
3 ctg123 . TF_binding_site 1000 1012 . + . ID=tfbs00001;Parent=gene00001
4 ctg123 . mRNA 1050 9000 . + . ID=mRNA00001;Parent=gene00001;Name=EDEN.1
5 ctg123 . mRNA 1050 9000 . + . ID=mRNA00002;Parent=gene00001;Name=EDEN.2
6 ctg123 . mRNA 1300 9000 . + . ID=mRNA00003;Parent=gene00001;Name=EDEN.3
7 ctg123 . exon 1300 1500 . + . ID=exon00001;Parent=mRNA00003
8 ctg123 . exon 1050 1500 . + . ID=exon00002;Parent=mRNA00001,mRNA00002
9 ctg123 . exon 3000 3902 . + . ID=exon00003;Parent=mRNA00001,mRNA00003
10 ctg123 . exon 5000 5500 . + . ID=exon00004;Parent=mRNA00001,mRNA00002,mRNA00003
11 ctg123 . exon 7000 9000 . + . ID=exon00005;Parent=mRNA00001,mRNA00002,mRNA00003
BED
Name
BED
Format
3 initial required fields and 9 additional optional fields. Fields are separated by a tab.
Required
- chrom - name of chromosome
- chromStart - Starting position in chromosome. First base in chromosome is numbered 0. This 0 based indexing is different from other formats that use a 1 based index.
- chromEnd - End position of feature in chromosome.
Optional
- name - Name of BED line.
- score - Score with range of
(0..1000). Can denote display indcations - strand - ‘+’ or ‘-’
- thickStart - The starting position at which feature is drawn thickly
- thickEnd - The ending position at which feature is drawn thickly
- itemRgb - RGB value example:
255,0,0which can denote color to display data in BED line. Should limit to 8 colors or less in file. - blockCount - Number of exons (blocks) in the BED line
- blockSizes - comma separated list of block sizes. Number of items in list should be equal to blockCount
- blockStarts - comma separated list of block starts. Values are relative to chromStart. Number of items should be equal to blockCount
Application Support
Source
USCS?
Example
chr1 213941196 213942363
chr1 213942363 213943530
chr1 213943530 213944697
chr2 158364697 158365864
chr7 127473530 127474697 Pos3 0 + 127473530 127474697 255,0,0
chr7 127474697 127475864 Pos4 0 + 127474697 127475864 255,0,0
chr7 127475864 127477031 Neg1 0 - 127475864 127477031 0,0,255
track name=pairedReads description="Clone Paired Reads" useScore=1
chr22 1000 5000 cloneA 960 + 1000 5000 0 2 567,488, 0,3512
chr22 2000 6000 cloneB 900 - 2000 6000 0 2 433,399, 0,3601