Quickstart

bedshape is composed of two subcommands, profile and alias.

Using the profile subcommand

profile is the subcommand handling the generation of mutational and reactivity profiles, plots; and shape files.

$ bedshape profile --reference /path/to/reference.fa \
        --modified modified.bam \
        --region chr11:65505800-65505900

Like shapemapper2, bedshape requires only a modified sample to work with. However, you may also pass a unmodified/untreated sample, and a denatured sample as well.

$ bedshape profile --reference /path/to/reference.fa \
        --modified modified.bam \
        --unmodified unmodified.bam \
        --denatured denatured.bam \
        --region chr11:65,505,800-65,505-900

The optional argument for the unmodified/untreated sample can be spelt as either --unmodified or --untreated. Note that commas are allowed in the region, as long as they come after the colon (:).

In lieu of a single region, bedshape can also take a BED file to produce outputs for all regions specified therein.

$ bedshape profile --reference /path/to/reference.fa \
        --modified modified.bam \
        --unmodified unmodified.bam \
        --bed interesting-genes.bed

Using the alias subcommand

You may often find yourself working with the same set of aligned reads, which reside in some far-away directory with a very long name. To avoid having to specify the location of these sets of files every time, bedshape supports the aliasing of these files.

$ bedshape alias add october-exp \
        --reference /path/to/reference.fa \
        --modified /data/october/modified.sam \
        --unmodified /data/october/unmodified.sam

Then, you may pass this ‘alias’ in place of --modified, -unmodified, and -denatured arguments in the profile subcommand.

$ bedshape profile --alias october-exp \
        --bed interesting-genes.bed