Bioinformatic File Cheatsheet

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.

  1. seqname - The name of the sequence. Must be a chromosome or scaffold.
  2. source - The program or database that generated this feature.
  3. feature - The name of this type of feature. Some examples of standard feature types are “CDS”, “start_codon”, “stop_codon”, and “exon”.
  4. start - The starting position of the feature in the sequence. The first base is numbered 1.
  5. end - The ending position of the feature (inclusive).
  6. score - A score between 0 and 1000. If no score, then ‘.’ is used
  7. strand - Valid entries include ‘+’, ‘-’, or ‘.’ (for don’t know/don’t care).
  8. 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”
  9. 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

  1. chrom - name of chromosome
  2. 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.
  3. chromEnd - End position of feature in chromosome.

Optional

  1. name - Name of BED line.
  2. score - Score with range of (0..1000). Can denote display indcations
  3. strand - ‘+’ or ‘-’
  4. thickStart - The starting position at which feature is drawn thickly
  5. thickEnd - The ending position at which feature is drawn thickly
  6. itemRgb - RGB value example: 255,0,0 which can denote color to display data in BED line. Should limit to 8 colors or less in file.
  7. blockCount - Number of exons (blocks) in the BED line
  8. blockSizes - comma separated list of block sizes. Number of items in list should be equal to blockCount
  9. 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
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