Welcome to Jamtools! A Python tool for working with SAM files created with SAM files (files resulting from mapped sodium bisulfite converted next generation sequencing data). Jamtools performs similar functions to the popular software tool Samtools, but simplifies the usage of many functions and improves upon the speed due Jamtool's lightweight nature.
Version: 1.0 License: MIT
Jamtools was created by J.D. Duryea (duryea@bcm.edu). Please feel free to ask any questions, voice concerns, or suggest improvements!
Installation is simple: just download the jamtools.py file and copy it to your working directory.
matplotlib numpy pylab
Currently, Jamtools offers only a handful of functions, but I'm constantly adding more! These function have been useful to us at Waterland labs and hopefully they can help you too!
All functions in Jamtools have the same commandline usage form: python jamtools.py command file.sam
count_reads:
counts the number of reads in a .Sam file
count_non_unique_mapping: counts the number of reads that did not map uniquely i.e. have a MAPQ score of 0
count_duplicates:
counts the number of duplicate reads (PCR and/or optical)
count_unmapped_reads:
counts the number of reads that did not map
get_RONUM:
returns the rate of non unique mapping (the number of reads that did not map uniquely/ the number of reads total) A note about unique reads, the term "unique" is rather vague, we only have for each read a MAPQ score in the range [0, 42], which is the -10log_10 probability of how likely an the read is not placed correctly. High MAPQ score = good. For this function we just return the fraction of reads that have a MAPQ score of less than 42.
get_mapping_report:
returns statistics about the MAPQ scores for the reads in the library. Saves a plot (png) showing the distribution of scores.
library_complexity:
Beta, creates a scatter plot of the percentage of the library analyzed vs the average RONUM of that sample.
full_report:
Beta, returns a whole bunch of statistics about the library mapping, most of them coming from the functions about