Customizing pipeline for cDNA-PCR runs rather than gDNA amplicons.

[callumparr]

I wanted to ask if this pipeline could be altered slightly to run with cDNA-PCR libraries. We have custom UMIs in both forward and reverse linkers to create dsDNA from total RNA. I see that the first step is to bin reads to their respective location in the genome defined by the coordinates in the bed file. For a few amplicons in a run this seems practical but for the cDNA library, i.e. whole transcriptome RNA-seq this maybe not depend on how granular we get with the coordinates. I guess I could use the gene_id level coordinates from an annotation file. Do you know of another pipeline that is more suitable to run with cDNA-PCR rather than gDNA amplicons?