This maybe a silly question, but I want to quantify the expression level of a specific transcript across many single-end fastq files. The transcript in question is a novel one, and I don't think its in the HG38 transcriptome. Using
salmon gives me the abundance of ALL transcripts in ONE fastq file. So,
Is there a way to quantify the expression level of a single transcript, across many fastq files (these are all different samples), other than running
salmonon each fastq file and then searching for my transcript of interest?
How can this be done for a transcript which is not in the reference transcriptome?