Linkreg
Linking candidate cis-regulatory elements to target genes
Installation
Open terminal and type following:
pip install Linkreg
Input & Output
Input:
- Gene expression data file, separated by '\t'. Format: gene by biosample. Example:
| chromosome | gene_start | gene_end | gene_id | strand | biosample1 | biosample2 | ... |
|---|---|---|---|---|---|---|---|
| chr1 | 50 | 60 | gene1 | + | 1.5 | 2.7 | ... |
| chr1 | 70 | 80 | gene2 | - | 3.1 | 1.8 | ... |
| ... | ... | ... | ... | ... | ... | ... | ... |
'gene1' and 'gene2' are the ids of the genes.
- Track data file, separated by '\t'. Format: cCRE by biosample. Example:
| chromosome | cCRE_start | cCRE_end | biosample1 | biosample2 | ... |
|---|---|---|---|---|---|
| chr1 | 100 | 150 | 0.3 | 0.4 | ... |
| chr1 | 300 | 320 | 0.6 | 0.2 | ... |
| ... | ... | ... | ... | ... | ... |
Output:
cCRE-gene link score files. Format: pair by biosample. Example:
| chromosome | gene_start | gene_end | gene_id | strand | cCRE_start | cCRE_end | biosample1 | biosample2 | ... |
|---|---|---|---|---|---|---|---|---|---|
| chr1 | 50 | 60 | gene1 | + | 100 | 150 | 0.9 | 0.7 | ... |
| chr1 | 70 | 80 | gene2 | - | 300 | 320 | 0.1 | 0.8 | ... |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
Example run
In your terminal, type
python3 Linkreg.py --expression_input ../data/expression.bed --tracks_input ../data/DNase.bed ../data/H3K4me1.bed --output ../results/example_results.bed
or the CLI
Linkreg --expression_input ../data/expression.bed --tracks_input ../data/DNase.bed ../data/H3K4me1.bed --output ../results/example_results.bed
In the python script, type
from Linkreg import Linkreg
Linkreg(expression_file='../data/expression.bed', track_files=['../data/DNase.bed', '../data/H3K4me1.bed'], output='../results/example_results.bed')
