run bwa on rstudio

Question

[Nemo]

Hello,

I am looking to find a way to run bwa (Burrows-Wheeler Aligner) on my fastq files on rstudio. I have uploaded the bwa zip file (downloaded from Fast and accurate long-read alignment with Burrows-Wheeler transform) in rstudio and tried to run the following command:

bwa.path <- "/folder1/user/bwa/"

system(paste0(bwa.path," bwa index -a bwtsw /folder1/user/ref1.fasta"))

However, it keeps getting me the error of No such file or directory. Is this the standard way to call bwa command on rstudio? (

[ATpoint]

Remove the whitespace in front of bwa in the system command but seriously, run this in terminal or via a workflow manager. This is nothing to be done from inside R. Non-standard and nothing to get used to.

[Nemo]

Thanks @ATpoint for your reply. Removing white space does not solve the problem. (I am asked to do it via R.)

[ATpoint]

/folder1 does not look like any standard path in the root dir in either Linux or macOS. That is probably wrong. cd into the folder with the bwa binary and type pwd, use that path. Same for the fasta.