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

(downloads) docker_10x_bamtofastq



depends libgcc-ng:


depends libstdcxx-ng:




You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

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

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `10x_bamtofastq/tags`_ for valid values for ``<tag>``)

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