README.md

In PLStenger/ReadFastQC: Catch Useful Informations Into FastQC Html Files Created by Galaxy.

ReadFastQC

Catch useful informations (e.g. the "Name", the "Date", the "Total Sequences", the "Sequences flagged as poor quality", the "Sequence length", the "%GC" and the adapters content) into FastQC html files created by the FastQC tool.

Installation from GitHub and loading

# may be useful : install.packages("devtools")
library(devtools)
install_github("PLStenger/ReadFastQC")
library("ReadFastQC")

Quick Start

Galaxy give you many FastQC files in zip. Unzip it in a folder.

Got to R, don't forget to "Get your working directory" into this previous folder.

Run this to catch the information for one FastQC file :

FastQCresults("HI.4112.002.D710---D501.X18_R2_fastqc.html") # for old FastQC version <2019
New_FastQCresults("HI.4112.002.D710---D501.X18_R2_fastqc.html") # for new FastQC version > 2019

Run this to catch all information for all FastQC files and print it in a file ("FastQCanalysis.csv") :

FastQCresultsForAll() # for old FastQC version <2019
New_FastQCresultsForAll() # for new FastQC version > 2019

Run this to obtain all adapters content of all FastQC in one pdf file ("Adapters content.pdf"), but before you will need to unzip all files :

id <- list.files(pattern = ".zip") # Find all the names of files with html extension
for(i in id){
  unzip(i, exdir="~/PATH_OF_FOUR_FILES")
}
adapter()

Run this to obtain all the per base quality of all FastQC in one pdf file ("Per base quality.pdf"), but before you will need to unzip all files :

id <- list.files(pattern = ".zip") # Find all the names of files with html extension
for(i in id){
  unzip(i, exdir="~/PATH_OF_FOUR_FILES")
}
bquality()

And that's it ! ;)

Update 2020/03/17

For new version of FastQC, lunch:

New_FastQCresults("HI.4112.002.D710---D501.X18_R2_fastqc.html")
New_FastQCresultsForAll()

PLStenger/ReadFastQC documentation built on April 3, 2021, 4:53 a.m.