I'm a novice at RNA-Seq data analysis, and I have a little experience using the command line to do things on my computer.
I'm using Kallisto to align fastq files for RNA-Seq. I know that it is possible to just write a shell script to apply Kallisto to all the fastq files I have in a folder, but I'm not exactly sure how to do this.
In pseudocode, I want to do this:
for [each file] in [directory]; do kallisto quant file_x > file_x_aligned; done
Where I'm stuck is in naming each of the output files uniquely. I'm sure there is an easy way to do this, but it's not coming to me. Sorry for the noob question. Any help would be greatly appreciated.