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A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs

This repository contains all the code that was used to perform the evaluations in the manuscript defining the JCC score:

Soneson C, Love MI, Patro R, Hussain S, Malhotra D and Robinson MD: A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs. bioRxiv (2018).

The main purpose of this repository is to provide a record of the analyses in our paper. All the results were obtained using the provided Makefile. Note, however, that reproducing the results requires installing all the software tools that were used, downloading the raw RNA-seq data as well as the annotation files, and subsequently setting the correct paths to these (typically done in the beginning of the master Makefile or any of the specific makefiles in the makefiles subdirectory).

Notes

The fasta_to_fastq.pl script was downloaded from https://code.google.com/archive/p/fasta-to-fastq/ on May 17, 2018.

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