This repository contains custom scripts and documentation associated with the analyses in our BioRxiv manuscript concerning the application of our TALON pipeline to long read transcriptomes from PacBio and direct-RNA Oxford Nanopore.
You can find the preprint here: https://www.biorxiv.org/content/10.1101/672931v1
To download the TALON program, please visit https://github.com/dewyman/TALON.
To download the TranscriptClean program, please visit https://github.com/dewyman/TranscriptClean.
To download the ENCODE DCC deployment of the TALON pipeline, please visit https://github.com/ENCODE-DCC/long-read-rna-pipeline.
plotting_scripts: Final versions of data visualization scripts used in the paper.
Figure_2: Describes exactly how the panels of Figure 2 in the paper were generated
Figure_3: Describes exactly how the panels of Figure 3 in the paper were generated
Figure_4: Describes exactly how the panels of Figure 4 in the paper were generated
refs: Contains instructions for downloading reference genomes, GENCODE annotations, and variant files. Also includes scripts we used to prepare input files for TranscriptClean and TALON initializations.
Illumina: Scripts for downloading short-read Illumina RNA-seq data from the ENCODE consortium and running Kallisto on them in order to perform short read quantification.
analysis_scripts: Older versions of visualization scripts for plotting things like gene/transcript expression correlations etc. We are in the process of deprecating this directory and moving final script versions to plotting_scripts instead.