mod_mappings file are splitted into 50000 reads and processed in parallel on a our bioinformatic cluster.
Submission files provided are based on HTCondor submission architecture and should be adapted to other environment.
The first script (nanoT_prep) split the mod_mappings.bam file into smaller bam files.
The second script (nanoT_parsing) extract the information from the Ml and Mm fileds of the bam file. This script also compute the mean of the BrdU signal per 1kb bin.
The third script (nanoT_merging) merge the per read 1kb binned signal into genomic 1kb bin.
The nanoT_bam2bed script created a compressed bed file containing all the chrom, start and end of the reads in order to check the genomic coverage of the experiment.
The nanoT_cleaning is used to clean data at the end of the procedure.
The nanoT_ParsingFunction.r script contains the function used in the nanoT_parsing script.
Examples of the output files are in the Zenodo repository under the DOI 10.5281/zenodo.12668295
To generate session_info file
library(sessioninfo)
session_info() %>% capture.output(file="nanotiming_processing_session_info.txt") A yml file is provided to recreate the r4nanoT conda env (r4nanoT_20240731.yml)