Discussion autour des formats de fichiers.
Les standards à utiliser, les bibliothèques, les bonnes pratiques.

Bed file

You are currently viewing a revision titled "Bed file", saved on 12 May 2017 at 13 h 44 min by Sébastien Letort
Title
Bed file
Content

Bed : Browser Extensible Data

Specifications

Officially none, but UCSC browser propose one that can be used : http://www.genome.ucsc.edu/FAQ/FAQformat.html#format1 Most prog (I've used) consider only the 3 first column (seq_id, start, end).

Warning :

UCSC spec. use 0-based coordinates, half-open region, not all prog consider this.

Samples

S1

chr7 127471196 127472363
chr7 127472363 127473530
chr7 127473530 127474697

S2

chr7 0 1 base_une

Recommended library

?

Recommended tools

bedops : https://bedops.readthedocs.io bedtools : bedtools.readthedocs.io

Comments

  • To load data I used a personal class RegionLink that aims to manage file like "chrom,start,end <=> chrom',start',end'" It can be found in https://gitlab.inria.fr/sletort/Brassica_scripts/blob/master/lib/RegionLink.py
  • Bedops propose the format starch which is a gzip bed with an integrated index, which is greatto work and save space.
Excerpt
Footnotes


Old New Date Created Author Actions
12 July 2017 at 11 h 17 min Sébastien Letort
12 May 2017 at 11 h 44 min Sébastien Letort