- recipe scramble
Soft Clipped Read Alignment Mapper
SCRAMble identifies clusters of soft clipped reads in a BAM file, builds consensus sequences, aligns to representative L1Ta, AluYa5, and SVA-E sequences, and outputs MEI calls
- package scramble¶
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install scramble and update with:: mamba update scramble
To create a new environment, run:
mamba create --name myenvname scramble
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).
Alternatively, use the docker container:
docker pull quay.io/biocontainers/scramble:<tag> (see `scramble/tags`_ for valid values for ``<tag>``)
SCRAMble runs as a two-step process. First cluster_identifier is used to generate soft-clipped read cluster consensus sequences. Second, SCRAMble.R analyzes the cluster file for likely MEIs. Custom wrapper script scramble.sh is provided to help setting location of SCRAMble.R script, and values for --install-dir and --mei-refs params.