motif_counter

Motif counter is a simple bash script that allows users to scan all reads contained in a bam file for a specific motif sequence repeated a number of times. Designed to look for the number of variant telomere repeats and reads in a whole genome sequencing dataset. The program prompts for a character string, and the number of times that string should be present in each read, then pulls out the data. Motifs can either be consecutive or uncoupled from each other across the read, and analysis endpoints include read number and percentage tables, compiled bam files with only motif-containing reads, or bam files with motif-containing reads together with their paired end.