FastQC in R
3 answers
Give the ShortRead package a try (http://bioconductor.org/packages/release/bioc/html/ShortRead.html)
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James Ashmore
Specifically, see the qa and report functions.
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Sean Davis
Here's a good study guide for some of the early techniques used! http://binf.snipcademy.com/lessons/sequencing-techniques And if you need help writing a thesis you can use paperwriting.
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ChristopherDrake72 •
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
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Why complicate life? Just download fastqc from their site and run it from command line on your terminal.
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.
you could run fastqc from R and generate integrated reprots using fastqcr
Why complicate life? Just use fastp to do the easiest and fastest way for QC and filtering.