I want to calculate how much is it possible to map reads with long polyA tails in their ends as it is very likely to be discarded by most of the mapping tools. So, I would like to simulate read mapping by designing reads with polyA tails and caculate their mappability index.
Can anyone help on how to calculate "mappability index" based on polyA (mismatch) length in the end. Is it the right direction to do or should I first trim polyA tails from unmapped reads and calculate mappability of trimmed reads towards the end of transcripts. I still guess there would be few which map on initial mapping and not captured in unmapped reads pool.
My main goal is to find different transcript ends of a single transcript in a single tissue/molecule/sample from its Rnaseq data.