I am running QC for bulk RNAseq and ran the following code:
base_dir <- "/data/dpag-paupar-kap1/mert4522/FASTQ/0.2Data2"
fastqc_dir <- "/data/dpag-paupar-kap1/mert4522/FASTQ/0.2Data2"
fastqc(fq.dir = base_dir, qc.dir = fastqc_dir, threads=4)
which for some reason is giving the following error:
sh: /home/mert4522/bin/FastQC/fastqc: No such file or directory
Warning: error in running command
I am running this via RStudio in a NoMachine window (remotely connecting to my University high performance computing server). I am mystified by this error message because I know that this file does not exist, which is why I specified a different filepath. The wd is set to /data/dpag-paupar-kap1/mert4522.
Any advice?
tried changing file locations and filepaths, installing and uninstalling fastqcr package