I'm using CUTADAPT to edit fastq files (from Illumina bulk RNA-seq) before alignment with two targets:
- removing adapters
- removing poly-A
I'm using terminal on a mac to execute the commands. I've managed to do it as an example on a single fastq but would like to do it on multiple fastq files. I understand it is more of a LINUX question but hopefully would manage to get some help.
All the best.