PISCES Documentation¶

PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.

Contents:

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.

digraph {
rankdir=TB;
abundance [label="<f0> TMM(TPM)|<f1> counts|<f2> transcript metrics", shape=record];
de [label="<f0> log2(fold-change)|<f1> p-value", shape=record];
qc [label="<f0> nucleotide metrics|<f1> genotype metrics", shape=record];
index [label="<f0> salmon index|<f1> gene-transcript mapping|<f2> transcript/intron/intergene models", shape=record];
"config.json" -> "pisces index" [arrowhead=none];
"metadata.csv" -> "pisces submit" [arrowhead=none];
"metadata.csv" -> "pisces summarize-expression" [arrowhead=none];
"metadata.csv" -> "pisces summarize-qc" [arrowhead=none];
"contrasts.csv" -> "pisces summarize-expression" [arrowhead=none];
"pisces submit" -> "pisces summarize-expression";
"pisces submit" -> "pisces summarize-qc";
"pisces summarize-expression" -> abundance;
"pisces summarize-expression" -> de;
"pisces summarize-qc" -> qc;
"pisces index" -> index;
index -> "pisces submit";
}

Fig. 9 Overview of PISCES workflow, demonstrating configuration file inputs and descriptions of processes and outputs for each PISCES subcommand (index, submit, summarize-expression and 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.