Quick Start

Environment set up and installation: Installation.

Detailed instructions: Tutorial.

Example data:

https://dl.dropboxusercontent.com/s/wrsxjimr6l96lcq/example-data.tar.gz

git clone https://github.com/tyjo/coptr
cd coptr

wget https://dl.dropboxusercontent.com/s/wrsxjimr6l96lcq/example-data.tar.gz
tar -xzvf example-data.tar.gz

# Set up the environment:
conda env create -f coptr.yml
conda activate coptr

# Install coptr
pip install .

# Index the reference database:
coptr index example-data/ref-db example-data/ref-db/example-index

# Map reads against the reference:
coptr map example-data/ref-db/example-index example-data/fastq example-data/bam

# Extract read positions:
coptr extract example-data/bam example-data/coverage-maps

# Estimate ptrs:
# Note the min-reads flag is optional. We recommend the default setting (5000 reads).
coptr estimate example-data/coverage-maps out.csv --min-reads 2500

# View the output:
cat out.csv

log2(PTR):genome_id/sample_id,ERR969281,ERR969282,ERR969283,ERR969285,ERR969286,ERR969428,ERR969429,ERR969430
l-gasseri-ref,,,,,,1.1840987863325785,1.1945539660363145,1.2879271469720541
e-coli-mag,1.2078623467253466,1.0375575947553943,0.9433005522894075,0.759132363901812,0.7846476652840171,,,