genome-comparator

Utility for Genome browser data comparison

Environment preparation

python3 -m pip install -r requirements.txt

Data preparation

In order to compare data, you need to:

1. Download QmRLFS finder analysis data via Genome Browser API

• e.g. with curl curl -L 'https://api.genome.ucsc.edu/getData/track?genome=hg19;chrom=chr11;start=65188245;end=65194245;track=hub_124277_RLFS' > qmrlfs.txt

2. Download input DNA sequence for R-loop tracker analysis

• e.g. with curl curl -L 'https://api.genome.ucsc.edu/getData/sequence?genome=hg19;chrom=chr11;start=65188245;end=65194245;' > chr11_raw.txt

3. Clean input sequence data (original response from Genome browser contains metadata aswell)

• using util.py module: python3 util.py (you have to change the path of a input file)

4. Run R-loop tracker analysis on bioinformatics server (follow help instructions)
5. Download bedgrahph format, change paths in the script according to your data and run genome_comparator.py

This process will be automatized in the next version, you will only have to provide following params for the analysis: chrom=chr11;start=65188245;end=651942454