This tool estimates the number of alignments that would be excluded from one or more BAM files given a variety of filtering criteria. This is useful for estimating the duplication rate in an experiment or more generally seeing what the effect of various option choices will be in other deepTools tools without actually spending the time to run them.
The output file is a simple text file with the following columns:
- Total reads (including unmapped)
- Mapped reads
- Reads in blacklisted regions (--blackListFileName)
The sum of these may be more than the total number of reads. Note that alignments are sampled from bins of size --binSize spaced --distanceBetweenBins apart.
For more information on the tools, please visit our help site.
For support or questions please post to Biostars. For bug reports and feature requests please open an issue on github.
This tool is developed by the Bioinformatics and Deep-Sequencing Unit at the Max Planck Institute for Immunobiology and Epigenetics.