i have data from a Rip-seq experiment between two samples from two different genotypes, and for each sample they did the sequencing for both the footprint (ribosomal protected fragments) and cytoplasmic input RNA and i am trying to estimate the ribosome density and perform Peak Calling on both but not sure where to start. The fastq files are already trimmed and aligned so i ended up with bam files but stuck on the next step. I did some research here and in other platforms and checked Piranah and the ripseeker R package but i couldn't find there an argument to include the input RNA to the Rip-seq data. My end goal is to compare the peaks of the ribosome-protected fragments of each genotype and to plot them against each other ( i would like to calculate the peaks based on the ratio of the ribosome-protected fragments to the fragments obtained by random fragmentation from the input RNA).
Can someone help me by pointing to a pipeline or a workflow with a similar sitting? Many thanks in advance