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