Hello!
We're going to run fastp to trim any adaptors and filter any low quality reads.
While I understand it's possible to run a process on all files in a directory using wildcards like so:
fastp -i ./*pass_1.fastq.gz #...
I'm not sure how to automatically make the output file names the same as the input file names, thus this script was needed! I believe this might be a way : https://itectec.com/unixlinux/bash-how-to-write-output-to-a-file-of-the-same-name-as-the-input/ but for want of time I'm going with python.
We can run BWA later in paired end read mode, so we won't merge reads.
Make sure to place yourself in the folder with all your gzipped fastq paired end reads first.
Also, make a folder called fastp inside that folder.
I could probably tell python to make it for you, but let's meet eachother halfway!
.°(ಗдಗ。)°.
I heavily referenced the approach of Erick Lu (https://erilu.github.io/python-fastq-downloader/#automating-downloads-using-python). I would also refer to the link if you want to try using python to automate getting data from SRA.
Dependencies:
- Python and modules
osandsubprocess - fastp
- multiqc
Have fun!