scPipeCPP

This pipeline provides tools for summarising gene counts from single or paired end reads containing unique molecular identifiers (UMI). Gene counting takes into account the UMI such that genes are only counted once per UMI for each exon.

Currently this software only supports macOS and Linux.

Installation

make
make install

Getting started

This pipeline contains 4 programs:

• sc_demultiplex
• sc_gene_counting
• sc_trim_barcode
• sc_exon_mapping

after make install. you can use make test to test the package. some test data and script will be in the test folder.

Run any of the programs with no arguments to see usage instructions.

Dependencies

• zlib (Should be present on all modern macOS or Linux versions)

TODO

• update UMI correction methods
• update basic_test.cpp and remove local path dependencies.
• simulate Drop-seq and MAR-seq data. and use them to test our pipeline.

Acknowledgements

This package is inspired by scater and scran packages. Output from this pipeline can be converted to SCESet class in scater for downstream analysis.