Nextflow script to generate counts starting from fastq files. Allow analysis of multiple samples at the same time
Options:
- --fastq [help = path to fastq files to parse to counts ]
- --genome [help = path to reference genome.fa ]
- --annotation [help = path to annotation.gtf ]
- --star_genome [help = path to folder with STAR reference genome]
If no STAR genome is has already built use this option
- --build_star_genome [help = optional to indicate to build STAR reference genome ]
Example:
nextflow RNAseqFastq2Counts.nf --fastq "path/to/fastq" --genome "path/to/ref.fa" --annotation "path/to/annotation.gtf" --star_genome "path/to/starGenome/dir" -with-report report.html
Options:
- -f , --folder [help = folder containing the file generated with feautureCounts *counts_matrix ]
- -o , --outputPath [help = output file path]
Example:
Rscript AggregateSamples.R --folder results/04_feauture_counts --outputPath test.csv