align shortreads using R

Question

[amroumouna]

I have this RNAseq project and it includes aligning short reads with the reference genome, I need to implement it using R and not any software

Is there any R package that does that? If not how do I do it?

[Rob]

Directly . . . in R? Unless you only have a tiny number of reads, I doubt you'll find any usable solution. R is absolutely not the right language for a tool implementing that type of functionality, and I doubt anyone has spent time in a serious effort to write an all-R short read mapper. That being said, there are packages (written in C++) for read mapping that expose an R interface. For example, I know that the subread aligner exposes an R interface.

[Chris Miller]

If you are trying to align sequencing data with R, you are doing it wrong.

[amroumouna]

@pierre do you know where I can find examples ofa genome and its fastq read file?

Answer 1

[Devon Ryan]

Rsubread: https://bioconductor.org/packages/release/bioc/html/Rsubread.html

Answer 2

[Pierre Lindenbaum]

http://www.genomebiology.com/2016/17/1/13#sec8 "A survey of best practices for RNA-seq data analysis" section "Mapping to a reference"