Pipelines for analysis of (non-umi based) single-cell and bulk RNA-sequencing data.
- pipeline_cram2fastq.py - convert CRAM files to Fastq format
- pipeline_scrnaseq.py - map, quantitate and qc RNA-seq data
These pipelines and scripts depend on the cgat-core pipeline system, which can be installed by following the instructions here: https://github.com/cgat-developers/cgat-core/.