Fastq-dump to featureCounts.sh
fastq-dump_to_featureCounts.sh is a bash script that…
- Downloads FASTQ reads from NCBI’s SRA using fastq-dump
- Indexes a reference genome and aligns reads to that index using bowtie2
- Converts the alignment file created by bowtie2 to BAM format and sorts it using samtools
- Assigns the read alignments to genes in a genome annotation file using featureCounts
Demonstration
This is a video demonstration of fastq-dump_to_featureCounts.sh.
During this demonstration, the full genome sequence and genome annotation for Saccharomyces cerevisiae S288C are used. The files example_nucleotide_sequence.fasta and example_genome_annotation.gtf are fragments of the nucleotide sequence and annotation for this genome. RNA-Seq reads for Saccharomyces cerevisiae (SRR8933512) are used as the example FASTQ files in this demonstration.
Usage
fastq-dump_to_featureCounts.sh [options] -a|--annotation <annotation_file> -f|--fasta <fasta_file> <SRR ID(s)>
This script downloads FASTQ reads from NCBI's SRA, aligns them to an annotated
genome using bowtie2, and generates gene count table(s) using featureCounts.
It can take a single SRR ID as an input, or multiple SRR IDs separated by
spaces.
Required arguments:
-a | --annotation input genome annotation file
-f | --fasta input FASTA file for annotated genome
SRR ID(s) Sequence Read Archive Run ID(s) (SRR...)
Optional arguments:
-h | --help show this help text and exit
-p | --processors number (n) of processors to use (default: 1)
--fastq-dump use 'fastq-dump' instead of the 'fasterq-dump'
--verbose make output of script more verbose
--removetemp remove read and alignment files once they are
no longer needed (minimises disk space needed)
--log redirect terminal output to log file