KREPA6 functions in RNA editing catalytic complex structural organization and gRNA utilization in T. brucei

Custom software package PARERS v2.0 (Pipeline for Analysis of RNA Edited RNA Sequences), was written using Python 3.12. This pipeline pairs and merges read sequences using BBMerge. Merged reads are checked for matching forward and reverse primer sequences so that any reads with mismatched primers can be excluded from downstream analyses. It can also take advantage of Unique Molecular Identifier (UMI) barcodes for the purposes of deduplication, so that only one instance of each UMI pair can be analyzed. Non-T (A/C/G) sequences are aligned to the corresponding A/C/G maxicircle sequence and any sequences containing a non-T mismatch can be excluded from analysis. Sequence alignments are generated by PARERS v2.0, and data output includes bar graphs and bubble plots made with R version 4.4.0.