The long and the short of it: unlocking nanopore long-read RNA sequencing data with short-read differential expression analysis tools

This repository contains the code used to perform the analysis and generate the figures in the paper published on NAR genomics and bioinformatics. Some intermidiate results of time- and resource-consuming tools are also provided.

The specific version of FLAMES used in this project can be accessed here.

• NSC contains the code used to analyze our NSC data.
  • Chen_et_al_2015_PNAS contains code to analyze the NSC short-read data. Other files under NSC are for the ONT long-read data.
  • preprocess contains the code to map the reads to the reference genome and do gene-level counting.
  • QC contains the code to calculate QC metrices and make QC plots for the NSC long-read data.
  • flames contains the script and config file to run FLAMES and SQANTI, and the code to plot the number of detected isoforms.
• sequins contains the code used to analyze our sequin data.
  • illumina contains the code used to analyze the sequins short-read data. Other files under sequins are for the ONT long-read data.
  • annotations contains the annotations for sequins, including decoy chromosome sequence, transcript sequences, GTF annotation file and gene/transcript length and abundance.

Our RNA-seq data can be accessed from Gene Expression Omnibus (GEO) under accession numbers GSE151984 (sequin ONT long-read data), GSE151841 (NSC ONT long-read data), GSE164598 (sequin Illumina short-read data) and GSE65747 (NSC Illumina short-read data from a previous study).