Scripts and notebooks for Gallman et al. 2026

This repository contains scripts and notebooks used to perform all data analysis in the manuscript

Gallman et al. (in preparation). "Comparative single-cell RNA sequencing brain atlas of larval Astyanax mexicanus surface and Pachón cavefish."

Prerequisites

Software

• cellranger v9.0.1
• cellbender v0.3.0
• scanpy v1.9.8

Input files

• Cellranger-ready reference genome, in ref/
• All reads in fastq format, in reads/
• Sample sheet formatted for Cellranger input and containing 'population' as additional metadata column (cave/surface), at samples.csv

Steps

1. Run CellRanger once per sample. This is presented as a SLURM array job here, but may need to be modified depending on your setup.
2. Run CellBender once per sample. This is also presented a a SLURM array job here.
3. Cluster using scanpy. This is performed in a Jupyter notebook.