Installation and Usage of the bamnado Package

Installation

Download a pre-built binary of the bamnado package from the releases page. Make sure to select the binary that matches your operating system and architecture. After downloading, you can place the binary in a directory included in your system's PATH for easy access. Alternatively, you can build the package from source using the following commands:

cargo install bamnado 

Usage

The bamnado package provides a command-line interface (CLI) for processing BAM files. Below is an example of its usage.

Example: Filtering Reads from a BAM File

Command

The following command filters reads from a BAM file based on specific criteria and writes the coverage to a bedGraph file:

bamnado bam-coverage \
  --bam input.bam \
  --output output.bedgraph \
  --bin-size 100 \
  --norm-method rpkm \
  --scale-factor 1.5 \
  --use-fragment \
  --proper-pair \
  --min-mapq 30 \
  --min-length 50 \
  --max-length 500 \
  --blacklisted-locations blacklist.bed \
  --whitelisted-barcodes barcodes.txt

Explanation of Options

• --bam: Path to the input BAM file.
• --output: Path to the output file (e.g., bedGraph or BigWig).
• --bin-size: Size of genomic bins for coverage calculation.
• --norm-method: Normalization method (raw, rpkm, or cpm).
• --scale-factor: Scaling factor for normalization.
• --use-fragment: Use fragments instead of individual reads for counting.
• --proper-pair: Include only properly paired reads.
• --min-mapq: Minimum mapping quality for reads to be included.
• --min-length: Minimum read length.
• --max-length: Maximum read length.
• --blacklisted-locations: Path to a BED file specifying regions to exclude.
• --whitelisted-barcodes: Path to a file with barcodes to include.

Output

The output file (output.bedgraph) will contain the normalized coverage data for the BAM file, filtered based on the specified criteria. BigWigs can also be generated by specifying the --output option with a .bw extension.

Additional Commands

Multi-BAM Coverage

To calculate coverage from multiple BAM files:

bamnado multi-bam-coverage \
  --bams file1.bam file2.bam \
  --output output.bedgraph \
  --bin-size 100 \
  --norm-method rpkm \
  --scale-factor 1.5 \
  --use-fragment \
  --proper-pair \
  --min-mapq 30 \
  --min-length 50 \
  --max-length 500

Split BAM File into Endogenous and Exogenous Reads

To split a BAM file into endogenous and exogenous reads:

bamnado split-exogenous \
  --input input.bam \
  --output output_prefix \
  --exogenous-prefix "exo_" \
  --stats stats.json \
  --allow-unknown-mapq \
  --proper-pair \
  --min-mapq 30 \
  --min-length 50 \
  --max-length 500

Split BAM File by Cell Barcodes

To split a BAM file based on cell barcodes:

bamnado split \
  --input input.bam \
  --output output_prefix \
  --whitelisted-barcodes barcodes.txt \
  --proper-pair \
  --min-mapq 30 \
  --min-length 50 \
  --max-length 500

Help

For more details on available commands and options, run:

bamnado --help