Code for Perez Mojica et al., 2023, STAR Protocols

Prerequisites

• Assumes a Linux or Mac environment and that you are working in the terminal.
• For other software requirements, see publication.

Steps to reproduce results in paper

0. Clone this repo and cd into the cloned folder.

1. bash 01_dl_and_index_dm6.sh

2. bash 02_dl_fqs_and_celseq_BCs.sh

3. i. bash 03_run_star.sh sample1 SRR21697060_1.fastq.gz SRR21697060_2.fastq.gz 16

   ii. bash 03_run_star.sh sample2 SRR21697059_1.fastq.gz SRR21697059_2.fastq.gz 16

4. Rscript --vanilla 04_make_counts_table.R

5. Rscript --vanilla -e 'rmarkdown::render("05_example_ep.Rmd")'