Brief Examples

Quantifying peak scores

BAMscale can quantify peaks in BED format from one or multiple BAM files. The output files are raw read counts, as well as FPKM, library-size and TPM normalized peak-scores (one file for each). A tutorial can be found here.

For more detail, go here.

When multiple samples (BAM files) are available, they should be processed together in one run.

Basic command (example)

./BAMscale cov --bed <preaks.bed> --bam <SAMPLE1.bam> --bam <SAMPLE2.bam> ... --bam <SAMPLEn.bam>

This will output four tables with the quantified peaks:

1) FPKM Normalization
2) Library Size Normalized
3) TPM Normalized
4) Raw Read Counts

Generating scaled coverage tracks

BAMscale can scale one (or more) BAM files to generate coverage tracks that are ready for visualization. This step generally takes ~3-5 minutes for standard ATAC-seq/ChIP-seq data, and ~20 minutes for genome sequencing data (100Gb in total size) using 4 threads.

A tutorial can be found here.

There is one main parameter here: BAM file(s).

The output of the command is a BigWig file. BAMscale "scale" function appends the ".bw" suffix to the end of the input file. For a BAM file named "sample.bam" the output will be:

sample.bam.bw

Basic Command (example)

./BAMcompare scale -t 4 --bam <BAM_1> (--bam <BAM_2> ... --bam <BAM_N>)

Output: Coverage track(s)s in BigWig format. If default scaling is used, samples can (and should) be processed separately, since data is scaled to the genome.