RNA-seq: identifying pericentromeric region

Question

[Polly]

Hi everyone, I'm new in bioinformatics and I'm currently trying to identify the pericentromeric region (satellites, families and sub-families) using RNA-seq (long non-coding and pair-end reads) data from samples from cancer patients. I'm not quite sure what the pipeline should be as this is my first time working with RNA-seq, what I'm currently trying to do is: I know that there are repeats with the sequence "TTGGA" that belong to this specific region, so I'm trying to do a manual search of the reads that contain at least 5 of these repeats to then check with IGV if they fall within the pericentromere. Has anybody worked with RNA-seq data and could help me out what the best pipeline to achieve this task should be? Thanks a lot in advance.