Hello, I'm rather new to this field so I'm mostly lost and looking for pointers in the right direction regarding information and documentation sources.
My end goal is to be able to determine the impact of (aberrant) alternative splicing events on the transcriptome of an individual. To do this I have come up with the following steps:
- From a reference GTF file extract all unique junctions. (.gtf file from gencodegenes)
- From a set of mapped reads, extract the splice-reads and junction information (also relevant to record the number of reads per junction for filtering purposes) (this is a .bam file with mapped reads from ENCODE)
- Based on reads and junctions, discern the following situations: annotated junction, exon-skipping, alternative 3', alternative 5' and novel junctions
However, I'm not familiar with the bioinformatics field at all and I'm at a loss for which technology/file types to use for each of the steps I'm considering. I apologize if my question is improper or goes out of scope for what should be asked here but I've been pulling hairs for the past couple of weeks and arriving nowhere. (if this is the case I'd appreciate a pointer towards where to start learning more on this field)