gene2bed

installation

$ git clone https://github.com/yyoshiaki/gene2bed.git

Data files are included.

usage

$ gene2bed.py -h                       
usage: gene2bed.py [-h] [-m MERGIN] species genelist output

Convert a gene list into a bed file.

positional arguments:
  species               human or mouse
  genelist              a gene list file
  output                output file

optional arguments:
  -h, --help            show this help message and exit
  -m MERGIN, --mergin MERGIN   mergin length

example

$ ./gene2bed.py mouse example/genelist.txt example/out.bed

input

genes.txt

Foxp3
Ctla4
Il2ra

output

chr1    60887000        60915832        Ctla4   0       +
chr2    11642807        11693193        Il2ra   0       +
chrX    7573644 7595245 Foxp3   0       +

references

• human : Gencode v30
• mouse : Gencode vM21

data preparation

Only for the admins.

bash prep_data.sh