README.md

Process Single Cell RNA sequencing data generated using the QIAseqUltraplexRNA kit

Jitao David Zhang, Feb 2019 : Adapted from [https://github.com/qiaseq/qiaseq-singlecell-rna]. The adapted version works with Python3 + conda, without dependency on Docker.

Major edits in the fork

• The code now works within an Conda environment with local intallation of STAR. No dependency on Docker is needed.
• intervaltree version 3.x is now used, use '.overlap' instead of '.search'
• Mixed indentation errors are fixed from the python code
• No shared memory is used given apparent difficulty and potential issues

Run the pipeline

sbatch qiagen-forSlurm.bash

Appendix

intervaltrees .search: .envelop or .overlap

Using .envelop caused many fewer reads annotated than using .overlap in find_genes.py. In fact, when I checked the intervaltree package in the docker file at https://github.com/qiaseq/qiaseq-singlecell-rna, it turned out the search function had strict=False, suggesting that overlap should be used rather than envelop.