Utility scripts for SLURM jobs.
List of stand-alone utilities:
- download_fastqs.sh - downloads FASTQ files from SRA repository with SRA Toolkit and perform quality control with FastQC
- fastqc_report.sh - performs quality control with FastQC and generates a MultiQC report
- download_bams.sh - downloads BAM files from SRA repository with SRA Toolkit and convert them to FASTQ files with bedtools
- star_index.sh - generates STAR index
- star_align.sh - performs RNA-sequencing data alignment to STAR index and generates gene counts, BAM files and bigwig files
- star_align_multi.sh - performs RNA-sequencing data alignment to STAR index using multiple FASTQ files per sample, and generates gene counts, BAM files and bigwig files
- generate_bigwigs.sh - sorts STAR-generated bedGraph files and converts them to bigWig files
- salmon_index.sh - generates Salmon index
- salmon_quant.sh - quantifies transcript abundances from RNA-sequencing data using Salmon
- salmon_quant_multi.sh - quantifies transcript abundances from RNA-sequencing data using Salmon for merged FASTQ files
- vast_align.sh - quantifies splicing from RNA-sequencing data using VASTdb database
- vast_combine.sh - combines vast-tools aling output into one table
- parse_bams.sh - parses BAM files for selected chromosomes
List of example config files:
- config.tab - config to download FASTQ or BAM files
- config_multi.tab - config to execute Salmon quantification and STAR alignment with multiple FASTQ files per sample
- merge.tab - config to merge vast-tools quantification files before combining into inclusion table
This project is under MIT License.