motif_counter
Program to pull out specific motifs from bam sequence files
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.