align shortreads using R
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8.7 years ago
amroumouna • 0

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?

RNA-Seq sequencing shortreads • 5.7k views
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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.

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

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

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8.7 years ago

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

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