merge aligned positionsmacros.xml
.. class:: infomark
**What it does**
This tool merges the overlapping aligned positions to define the read concentrated loci. If an annotation GTF file produced, the transcriptomic alignment positions are first converted to their corresponding genomic positions.
**Inputs**
* Alignments in BED format
* An annotation GTF file contaning reference genomic positions.
**Output**
* BED file containing the alignments with reads categorized into segments depending on which part of the read is aligned.
* Tabular file containing merged alignments. 4th column contains all the alignments merged into that location.