/RNAseqFastq2Counts

RNAseqFastq2Counts

Primary LanguageNextflow

RNAseq from fatsq to counts

Nextflow script to generate counts starting from fastq files. Allow analysis of multiple samples at the same time

RNAseqFastq2Counts.nf

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

AggregateSamples.R

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