Improving genome-wide mapping of nucleosomes in Trypanosome cruzi

bioRxiv pre-print

paper

These scripts require already installed software listed here

Custom configuration values should be set here

Repository outline

The source directory contains

• main.R - Entry point
• pipeline - scripts for each step involved in nucleosome data analysis
• common - configuration and helpers scripts

The data directory contains

• genomes - genomes fasta files
• overrepresented sequences in analyzed samples in fasta format
• UTRme output defining positions for value of plot2DO --sites

The output directory contains

• qc_output - fastqc output for each sample
• alignment - summary of alignments for each strategy (bowtie2, hisat2) and each sample
• alignment_summary - csv files for consolidated alignment data
• plots - plot2DO output for each strategy (bowtie2, hisat2) and each sample

Pipeline

Available steps:

• preprocess
• align
• convert_to_bam
• plot
• summary_tables
• convert_to_bigwig

Suggested Pipeline

1. main('preprocess')
2. main('align')
3. main('summary_tables')
4. main('convert_to_bam')
5. main('plot')
6. main('convert_to_bigwig')