read_count.py - script for counting human and fungal reads
This script counts the number of reads/alignments which are mapped to human and C. albicans, when sequencing combined samples (i.e. clinical samples of candidiasis). As an input, the script expects a file listing the bam files (i.e. "file_list.txt"), for example:
sample_1.bam
sample_2.bam
sample_n.bam
plotting_stats_fungi.R - script for plotting the obtained results (comming soon).
This script is written in R and reproduces the main plots of the study "Multiplexed target enrichment of coding and non-coding transcriptomes enables studying Candidaspp.infections from human derived samples" by Hovhannisyan et al, 2021. The initial data files are available upon request.