Commit 266bb3ef authored by Jeremy Mathews's avatar Jeremy Mathews

Update changelog and docs

parent 044e65cc
Pipeline #8289 passed with stages
in 5 minutes and 28 seconds
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**Background**
* Update scripts to reflect spaceranger or cellranger input
* Update CI to include simple3 and add simple3 tests for later pytest use (commented out for all simple CI)
* Add simple3 to test data folder
* redo channels to include multple rangers
*Known Bugs*
* cellranger mkfastq will not accept spaces in path for run param even if quoted, issue raised on 10XGenomics/cellranger github issue [#31](https://github.com/10XGenomics/cellranger/issues/31)
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10x Genomics scRNA-Seq (cellranger) mkfastq Pipeline
10x Genomics scRNA-Seq mkfastq Pipeline
====================================================
Introduction
------------
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 various ranger mkfastq tools 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.
FastQC is run on the resulting fastq and those reports and bcl2fastq reports are collated with the MultiQC tool.
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4. **cellranger**:
* 10x Genomics cellranger mkfastq [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/mkfastq](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/mkfastq)
6. **spaceranger**:
* 10x Genomics spaceranger mkfastq [https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/using/mkfastq](https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/using/mkfastq)
5. **bcl2fastq**:
* Ilumina's bcl2fastq [https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html](https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html)
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* fastqc [https://www.bioinformatics.babraham.ac.uk/projects/fastqc/](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
7. **MultiQc**:
* Ewels P., Magnusson M., Lundin S. and Käller M. 2016. MultiQC: Summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32(19): 3047–3048. doi:[10.1093/bioinformatics/btw354](https://dx.doi.org/10.1093/bioinformatics/btw354)
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* Ewels P., Magnusson M., Lundin S. and Käller M. 2016. MultiQC: Summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32(19): 3047–3048. doi:[10.1093/bioinformatics/btw354](https://dx.doi.org/10.1093/bioinformatics/btw354)
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