on a BED file genetrack_indexer.py -i $input -o $output -s $shift -v 0 -f BED -x Select input bed file Shift at 5' end **Help** This tool will create a visualization of the bed file that is selected. **Parameters** - **Shift at 5' end** should be used when the location of interest is at a fixed distance from the 5' end for **all sequenced fragments**! For example if the sequenced sample consists mono-nucleosomal DNA (146bp) we should expect that each nucleosome midpoint is located at 73 bp from the 5' end of the fragment. Therefore we would enter 73 as the shift parameter. Once corrected the reads on each strand will coincide and indicate the actual midpoints of the nucleosomes. When shifting the averaging process in GeneTrack is able correct for longer or shorter than expected fragment sizes as long as the errors are reasonably random.