xmap2bed12.pl_example.rmd

Applying the xmap2bed12.pl and xmap2bed.pl scripts to a xmap sample data
==========

A test data was extracted from some xmap file generated with Irys as well as the graphical representation of all cmaps aligning to the test scaffold.
![xmap example](pictures/xmap_example.png)

![BED5 and BED12 converted data](pictures/xmap2bed12_example.png)

The first track was obtained with **xmap2bed12.pl** while the second track was generated with **xmap2bed.pl** (only matching regions are reported in the latter).

After conversion and loading in IGV, the top track shows the BED12 export where thiner blocks represent regions of the query that do not align to the reference. The thicker blocks in both tracks represent the region of the reference that is matched in the query cmap (but differences in size within this region are not represented). Confidence filtering is also possible with the optional parameter '-x'.


<h4>Please send comments and feedback to <a href="mailto:nucleomics.bioinformatics@vib.be">nucleomics.bioinformatics@vib.be</a></h4>

------------

![Creative Commons License](http://i.creativecommons.org/l/by-sa/3.0/88x31.png?raw=true)

This work is licensed under a [Creative Commons Attribution-ShareAlike 3.0 Unported License](http://creativecommons.org/licenses/by-sa/3.0/).