Given a BAM file this tool calculates the number of times each read (=genomic region) is identified, and removes the ones for which the count number is under the user defined threshold.
The tool takes as input a BAM file with reads that have been aligned to a reference genome, so that genomic location information for each mapped read is available. Depending on how the 'Merge overlapping reads' parameter is set, the counts are calculated so that all reads mapping to exactly the same location are summed up, or all the reads that start or/and end at the same genomic position are summed up. The latter option is set by default since it greatly reduces redundancy in the counts data.
edgeR-input.tsv: A text file with counts for each genomic region, together with chromosome location info, suitable as input for tools like edgeR or DESeq.