This script converts a bam file into a PDF file with multiple plots including reads as well as damage informations.
The plots were hilghy inspired from the ameta outputs (Pochon et al 2024).
You will need Amber, Picard, samtools, PDFtools as well as multiple python packages (see header of the .py script) to be installed.
python3 Make_multiple_plotV2.py -b Yersinia_pestis_control.bam
- NoDup_sorted_filterBAM_quality_filtred_Yersinia_pestis_control_dna_damage.csv : CSV file output with many important informations.
- NoDup_sorted_filterBAM_quality_filtred_Yersinia_pestis_control_dna_damage.pdf : PDF file output with the plots.
Other files correspond to amber and pydamage outputs.