- recipe scramble
Soft Clipped Read Alignment Mapper
- Homepage:
- License:
CC
- Recipe:
- Links:
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¶
-
- Versions:
1.0.2-0
,1.0.1-2
,1.0.1-1
,1.0.1-0
- Depends:
bioconductor-rsamtools
>=2.4.0
htslib
>=1.15.1,<1.16.0a0
libgcc-ng
>=12
r-base
>=4.0.3
r-optparse
>=1.6.6
r-rblast
>=0.99.1
r-stringr
>=1.4.0
- Required By:
Installation
With an activated Bioconda channel (see set-up-channels), install with:
conda install scramble
and update with:
conda update scramble
or use the docker container:
docker pull quay.io/biocontainers/scramble:<tag>
(see scramble/tags for valid values for
<tag>
)
Notes¶
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.
Download stats¶
Link to this page¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/scramble/README.html)