rnaseq.sh: Run nf-core rnaseq pipeline
Usage: ./rnaseq.sh [options]
Options:
-o <output_dir> Set output directory (default: './results')
-r <raw_data_dir> Set raw FastQ file directory (default: './fastq_files')
-s <samplesheet> Provide an existing samplesheet CSV file
-i <sample_id_file> Provide a file containing sample IDs to generate the samplesheet
-v variant=true Execute variant calling with gatk
-h Display this help message
Either the -s (samplesheet) or -i (sample_id_file) option must be provided, but not both.
For -i, the sample_id_file should contain one sample identifier per line.
The samplesheet will include columns: 'sample', 'fastq_1', 'fastq_2', 'strand' (auto by default).
Example:
./run_rnaseq.sh -i /path/to/sample_ids.txt
./run_rnaseq.sh -s /path/to/existing_samplesheet.csv
./run_rnaseq.sh -i /path/to/sample_ids.txt -o /path/to/output_directory
differentialabundance.sh: Differential expression of genes starting from salmon counts analysis
Usage: ./gene_differentialabundance.sh <CASE> <CONTROL> <MATRIX> <GENE_LENGTH>
-o <output_dir> -n <project_name> -f <fastq_dir> -g <gtf_file> -w <work_dir>
-t <transcript_true>
Required Arguments (Positional):
1. CASE - File containig case ids
2. CONTROL - File containig control ids
3. MATRIX - Gene/Transcript count file from rnaseq
4. GENE_LENGTH - Gene/Transcript length file from rnaseq
Optional Flags:
-o OUTDIR Output directory
-n NAME Project name
-f FASTQ_DIR Fastq directory
-g GTF_FILE GTF file
-w WORK_DIR Work directory
-t TRANSCRIPT=true Transcript Differential Abundance
-h Display this help message