I have RNA-seq alignments stored in a .bam file, which were generated using Minimap2, along with an annotation file (Mitos_annotation.bed) for the mitochondrial genome. My goal is to reconstruct and visualize the mitochondrial primary transcript, including:
The sequential arrangement of genes. Cleavage sites at tRNA junctions. Polyadenylation (PolyA) sites for mRNAs. However, I am confused about the exact steps required to achieve this. Specifically:
- How can I identify and confirm cleavage sites from my BAM file and coverage data
- What tools or methods should I use to reconstruct the full-length primary transcript?
- How can I create a schematic diagram to represent processing events (e.g., tRNA cleavage, PolyA additions)?
I am struggling to integrate the alignment data with the annotation file to generate a meaningful representation of the primary transcript and its processing events. Could someone guide me through the necessary steps or suggest an efficient pipeline to accomplish this? Any help with commands, tools, or visualization techniques would be greatly appreciated.
