I'm currently trying to learn RNA-seq data analysis and differential expression in R. I've been using the Combine lab tutorial.
Everything was running well until the tutorial asked to use the
propmapped function (on this page) on my BAM files and then view the promapped proportion for each sample. In this tutorial we should be getting promapped proportion ranging from 0.05 to 0.150, however in my case I have no reads that align to my mapped genome (promapped = 0 in my case, for each sample). I don't know why as I've been using the data they provided for this tutorial.
I was wondering if someone could follow the first few steps of this tutorial until the propmapped step and tell me if they eventually get the right proportion of reads or not after the propmapped function. This could tell me if the tutorial is the culprit or not.