- recipe 10x_bamtofastq
Tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that can be used as inputs to re-run analysis
- package 10x_bamtofastq¶
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 10x_bamtofastq and update with:: mamba update 10x_bamtofastq
To create a new environment, run:
mamba create --name myenvname 10x_bamtofastq
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/10x_bamtofastq:<tag> (see `10x_bamtofastq/tags`_ for valid values for ``<tag>``)