on a BED file
genetrack_indexer.py -i $input -o $output -s $shift -v 0 -f BED -x
**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.