This repository contains code used for analysis of iPSC-derived sensory neurons, as described in this manuscript:
Molecular and functional variation in iPSC-derived sensory neurons http://www.biorxiv.org/content/early/2017/01/06/095943
The code includes:
- Example pipeline for aligning RNA-seq reads, and quantifying expression
- Calling eQTLs and splice QTLs with FastQTL, RASQUAL, and leafcutter
- Many of the analyses described in the paper
- analysis - scripts to analyse processed sensory neuron data
- data - input data for analyses (e.g. sample metadata)
- pipeline - scripts to process raw data, e.g. alignment, quantification
- utils - utility scripts
- supp - supplementary tables from the paper
Scripts within these directories may refer to files that are not part of the Github repository. Aligned BAM files are available from EGA (EGAD00001003145, 80 managed-access RNA-seq samples) or from ENA (accession ERP020576, 51 open-access RNA-seq samples). Similarly, ATAC-seq data for 8 and 23 managed and open-access samples are available. Summary statistics and gene expression counts are available at https://www.ebi.ac.uk/biostudies/studies/S-BSST16. Expression counts are not provided in the github repository, as they are available at the biostudies link above. Also, only expression counts for open-access samples could be provided.
This directory includes mainly R scripts used for high-levels analyses, including producing figures in the paper.
This directory includes sample metadata.
This directory includes scripts related aligning reads, computing gene expression counts, and calling expression QTLs and splice QTLs.
This directory includes support scripts for pipelines, such as for submitting jobs to our computing cluster, running other software tools, and processing the results.