Hello everyone!

I need your advices on described below topics:

1. I have a task to subset bam-files by read length. So, it is required to have only mapped reads with length between 26-34 bp. This is some kind of ribosome profiling experiments, so I want to retent only reads of described above length.

2. This reads also have some variants (SNV) in the defined positions. Is it possible to obtain infromation in data.frame-like view releted the distribution of these SNV across the length of these reads.

Thank you in advance, Best wishes, Alexander

One possibility for filtering is to use Rsamtools::filterBam(); see the help page for initial instructions.

Perhaps for SNV Rsamtools::pileup() will be helpful?