align shortreads using R
2
0
Entering edit mode
8.1 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 • 5.3k views
ADD COMMENT
2
Entering edit mode

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.

ADD REPLY
1
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
2
Entering edit mode
ADD COMMENT
2
Entering edit mode
8.1 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"

ADD COMMENT

Login before adding your answer.

Traffic: 2298 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6