bamutils / expressed

Finds regions expressed in a BAM file

This will scan a BAM file, looking for regions of mapped reads. The found
regions are output in BED format. These regions are found in a model-free
manner, so they may represent novel or known transcripts. This is also helpful
for peak-finding in ChIP-seq experiments.

Usage: bamutils expressed {options} bamfile

-ns             Ignore strandedness when creating regions
                (default: false)

-uniq           Only use unique starting positions when performing counts
                (default: false)

-dist N         minimum distance required between regions - they will be
                merged if w/in this distance
                (default: 10)

-mincount N     The minimum number of reads required in a region
                (default: 2)