Appendix
=================

Data
----------------

The *data* directory contains several types of data:

- Genometable files for several species. To generate genometable files for other species (and genome builds), use ``makegenometable.pl`` that can be found in the *scripts* directory as follows::

        makegenometable.pl genome.fa > genometable.txt

- Ideogram files for visualization of chromosomes in **GV** command.
- Mptable files that describe the mappable bases of each chromosome.


Mappability files
-----------------------------------

DROMPAplus accepts the mappability files generated by scripts provided by `MOSAiCS <http://www.stat.wisc.edu/\~{}keles/Software/mosaics>`_, which is based on the code from Peakseq.
The binary mappability files (**chr*_map_binary.txt**) can be generated by using the MOSAiCS scripts with the appropriate fragment length and bin size (here, 150 bp and 100 bp, respectively).

Next, gzip and modify the filenames for DROMPAplus::

    for i in $(seq 1 22) X Y M; do
       gzip chr${i}_map_binary.txt
       mv chr${i}_map_binary.txt.gz map_chr${i}_binary.txt.gz
    done

After this, make the "mappability table", a tab-delimited file describing the number of mappable bases for each chromosome, using ``makemappabilitytable.pl`` found in the *otherbins* directory::

    $ makemappabilitytable.pl genometable.txt map > mptable.txt

where the second argument "map" is the prefix of binary mappability files.

Gene-density files
--------------------------

Gene-density files can be generated through ``makegenedensity.pl`` found in the *scripts* directory.
To use a 500-kbp window, type::

     $ makegenedensity.pl genometable.txt refFlat.txt 500000

and the gene-density files ``chr*-bs<binsize>`` will be generated in the current directory. 
These data for several species can also be downloaded from the DROMPAplus website.

Next, make a new directory for the gene-density files::

    $ mkdir gene_density_hg19
    $ mv chr*-bs* gene_density_hg19

The gene-density files can be specified as follows::
 
    $ drompa+ GV $s1 $s2 $s3 $s4 -o ChIPseq-wholegenome --gt genometable.txt \
      --GD gene_density_hg19/ --gdsize 500000