This pipeline is a wrapper for the cellranger mkfastq tool from 10x Genomics (which uses Illumina's bcl2fastq). It takes bcl's and demultiplexes samples from 10x Genomics Single Cell Gene Expression libraries into fastqs.
This pipeline is a wrapper for the cellranger mkfastq tool from 10x Genomics (which uses Illumina's bcl2fastq). It takes demultiplexes samples from 10x Genomics Single Cell Gene Expression libraries into fastqs.
FastQC is run on the resulting fastq and those reports and bcl2fastq reports are collated with the MultiQC tool.
...
...
@@ -48,19 +48,22 @@ To Run:
* run name, puts outputs in a directory with this name
* eg: **--name 'test'**
***--bcl**
*Base call files (tarballed [*.tar] +/- gunzipping [*.tar.gz] from a sequencing of 10x single-cell expereiment, supports pigr parallelization).
*There can be multiple basecall files, but they all will be demultiplexed by the same design file.
*base call files (tarballed [*.tar] +/- gunzipping [*.tar.gz] from a sequencing of 10x single-cell expereiment, supports pigr parallelization)
*there can be multiple basecall files, but they all will be demultiplexed by the same design file
description = 'This pipeline is a wrapper for the cellranger mkfastq tool from 10x Genomics (which uses Illuminas bcl2fastq). It takes bcls and demultiplexes samples from 10x Genomics Single Cell Gene Expression libraries into fastqs.'