Naive and primed pluripotency in human ESCs

Overview

This repository provides the code for the paper Transcriptional heterogeneity in naive and primed human pluripotent stem cells at single-cell resolution, by Messmer et al. (2019).

Generating the results

To reproduce the analyses from count matrices:

1. Enter data/ and run download.sh to download all relevant count tables.
2. Enter analysis/ and run run_main.sh to compile all of the analysis scripts.
3. Enter figures/ and run make_figures.sh to create all of the figures used in the manuscript.

Realigning the sequence data

To reproduce the analyses from the FASTQ files:

1. Follow the instructions in genomes/builds/README.md to build the genome indices. Similarly, follow the instructions in genomes/annotation/README.md to obtain the annotation.
2. Download the FASTQ files from ArrayExpress. Files corresponding to each batch of data should be placed in data/real-2383_20161024/fastq, etc.
3. Run the various mapme.sh scripts to execute the master scripts for alignment, and count_me.sh for read counting. Paths should refer to the top-level tools/ directory obtained using download.sh.