Hello Biostars community,
When running salmon or star_salmon, are sample's “independent” from one another during quantification in or any step for that matter during the process from fastq to quant.sf?
The reason I ask is because I am running my samples through nf-core/rnaseq pipeline version: 3.8.1, which generates a multiqc report. I see that some samples are of lower quality (aren't that great relative to the others.) I am thinking of simply just removing the "bad sample" folders from the salmon or star_salmon directory, and importing through tximport. I will do this if the pre-processing of samples are independent from one another (that one sample does not rely on another during the quantification process or other pre-processing steps)? Otherwise, I was thinking to remove those low quality sample fastq files and re-run nf-core/rnaseq, which really seems excessively unnecessary, hence this question.
I think the process is independent, because I recall that when I was running salmon "manually" previously (without an nf-core pipeline), I remember, there was a salmon command for each sample, I even see this in the nf-core/rnaseq pipeline as well?
Thank you in advance, Pratik
