I have a bunch of FASTQ files (10 samples). I try to load them in R for mapping them but I cannot figure out how to do For example, Dseq2 requires bat files and not fastq, so I cannot find the way how to import fastq and analysis
I tried to use Rsubread 1.26.1 but for example after I do the following command I get this error ERROR: the output directory is not writable, but the index builder needs to create temporary files in the current directory. Please change the working directory and rerun the index builder.
I do setwd() to a good place but still I get error
Can someone comment how to start the analysis for Fastq files ?