FastQC in R

Question

[rjames]

I am beginning a RNA seq analysis and would like to check the quality of the data. Are there any R language packages that can produce the sequence quality analyses that FastQC performs (such as Fastqc in Galaxy)?

[Santosh Anand]

Why complicate life? Just download fastqc from their site and run it from command line on your terminal.

[rjames]

Actually, it would be less complicated to do it in R as part of a R workflow. So I am still interested in finding if there are any equivalent packages in R. If not, the command line FASTQC is still an option. Thanks for your reply.

[russhh]

you could run fastqc from R and generate integrated reprots using fastqcr

[chen]

Why complicate life? Just use fastp to do the easiest and fastest way for QC and filtering.

Answer 1

[James Ashmore]

Give the ShortRead package a try (http://bioconductor.org/packages/release/bioc/html/ShortRead.html)

[rjames]

I will check out ShortRead later this afternoon.

[Sean Davis]

Specifically, see the qa and report functions.

Answer 2

[eculfa]

Hello!!

A group in Brazil recently published a workflow involving a package called "Rqc" to perform quality control in R.

Check it out from here. https://bioconductor.org/packages/devel/bioc/vignettes/Rqc/inst/doc/Rqc.html