I've recently downloaded the FastqCLeaner to process paired-end fastq files locally using R (4.0.3). I'm having trouble with the shiny app. It is not uploading my second fastq file, and is repeated asking for file 1. Can someone help me? is there another package i can use for trimming and alignment in R? I've tried GREP2 but had massive installation issues, i wasted 2 days trying to install in R.
$\begingroup$ Ditch R, it's not the proper environment for handling reads. R is for statistical analysis and plots and absolutely nothing else. $\endgroup$– Devon RyanDec 23, 2020 at 16:19
2$\begingroup$ Can you clarify what tasks need to be done on those files? There is most likely a simple command line tool that handles this in like no time without the need to bother with R-ish tools here. $\endgroup$– user3051Dec 23, 2020 at 19:40