Advanced Rmarkdown templates for generating Next Generation Sequencing reports. The reports are stand alone, interactive html documents which include various quality metrics about the fastq reads and the mapping of the reads to the reference genome.
Clone this repository with
git clone https://github.com/angelovangel/ngs-reports.git
Open the respective Rmarkdown file in RStudio and click on Knit then Knit with parameters. Fill in the required fields and then press the Knit button. The generated report is a standalone html page with the same name as the Rmarkdown file, e.g. 02-RNAseq.Rmd will generate 02-RNAseq.html.
The required R packages will be installed if they are not available when you first run the pipeline. In addition, these external programs have to be available in your path:
You can also use the environment.yml file to create a conda environment with the required tools, and then start Rstudio in that environment:
conda env create -f environment.yml
and then activate it with:
conda activate ngs-reports
Start RStudio: on Linux rstudio, on MacOS open -na Rstudio. Check that the $PATH is set correctly in RStudio - Sys.getenv("PATH") should give the same as echo $PATH on the command line.
This template generates some quality metrics about a bunch of fastq files - total output, number of reads, percent of bases with a phred score > than Q20 and Q30, GC-content.
In addition to the FASTQ quality metrics, this template generates also: alignment quality of the reads to the reference genome, summarization metrics of the assignment of the reads to genome features, duplication rate, read strandness, gene body coverage.
IMPORTANT - if using prokka for annotation, remove the "|" from both the fasta header and from the gff files!!! Otherwise Rsubread will fail.