This repository contains the scripts used to preprocess and align RNA-seq reads to a genome for publication ""

The order of script execution is as follows:
1) mkdirs_for_samples_raw_data.sh
This code makes the directories for both reads of each sample and makes a sample.txt containing all the sample names. This is used for preprocessing.

2) hts_preproc_SCRI_ROOT_RNAs.slurm
This slurm script runs the entire preprocessing pipeline.

3) References/rbind_genomes.sh
This script is mainly for documentation purposes. It combines the .fna and .gtf files for the J. microcarpa and J. regia genomes.

4) star_index_combined_genomes.slurm
Slurm script to index the custom genome file.

5) star_alignment_SCRI_ROOT_RNAs._2pass.slurm
Slurm script to perform alignment of processed reads to custom genome.

6) generate_counts_tbl.sh
Bash script to generate a counts table of all samples and genes