How to use umicount

This section explains how to use the umicount to remove PCR duplicates from a BED12 file.

First you will have to make sure that umicount is correctly installed. See Install for more information.

If you don’t know how to generate a valid BED12 file for umicount, you can refer to the Recommendations.

Working with a single bed file

Just specify the path to a BED12 formatted file with the -f argument:

umicountFP -f ./your_bed12_file.bed

Working with multiple files

Just specify the path to the folder containing your BED12 formatted files with the -d argument:

umicountFP -d ./path/to/your/bed12_formatted_files/