PISCES Documentation¶
PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.
Quickstart¶
Install the python module (see Installation instructions)
Create transcriptome and genome index files (see pisces index)
Create a CSV file to define your experiment (see PISCES metadata file format)
Submit your jobs to a DRMAA aware high performance computing cluster (see pisces submit)
Summarize gene/transcript expression and QC metrics in analysis-ready tables using pisces summarize-expression and pisces summarize-qc.
Publication¶
The manuscript is available on bioRxiv and the latest version can be viewed in this documentation: PISCES: a package for rapid quantitation and quality control of large scale mRNA-seq datasets.
Matthew D Shirley, Viveksagar K Radhakrishna, Javad Golji, Joshua M Korn. PISCES: a package for rapid quantitation and quality control of large scale mRNA-seq datasets. bioRxiv. 2020.
Development¶
Pull requests and issues are welcomed on the pisces Github repository.