Here we provide the 10X Genomics Cell Ranger pipeline to enable processing of data generated by 10X Chromium single cell 3’ library construction (v2; single cell transriptomics) assay and submitted to this Data Portal. Note that this pipeline has not been approved by the HCA project, but we make it available for the community to use while we finalize development and approval of our 3 prime Optimus pipeline.
The source code for the pipeline is available in this repository, and was kindly provided by 10X Genomics. The docker image we use to run the pipeline is here (dockerfile). Note that the reference transcriptome used is Gencode GRCh38, which is consistent with our other pipelines.