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*Region list
*Region list
If the interest of qplot is a list of regions, e.g. exons, this can be achieved by providing a list of regions. The regions should be in the form of "chr start end label" each line in the file. In order for this option to work, within each chromosome (contig) the regions have to be sorted by starting position, and also the input bam files have to be sorted.
If the interest of qplot is a list of regions, e.g. exons, this can be achieved by providing a list of regions. The regions should be in the form of "chr start end label" each line in the file (NOTE: ''start'' and ''end'' position are inclusive and they follow the convention of [http://genome.ucsc.edu/FAQ/FAQformat#format1 BED file]).
In order for this option to work, within each chromosome (contig) the regions have to be sorted by starting position, and also the input bam files have to be sorted.
For example, you can create a text file, region.txt like following:
1 100 500 region_A
1 100 500 region_A
1 600 800 region_B
1 600 800 region_B
2 100 300 region_C
2 100 300 region_C
...
Then specifying <code> --regions region.txt</code> enables qplot calculate various statistics out of sequenced bases only from this region.
Qplot also provides the <code>--invertRegion</code> option. Enabling this option tells qplot to operate on those sequence bases that are outside the given region.
Qplot also provides the <code>--invertRegion</code> option. Enabling this option tells qplot to operate on those sequence bases that are outside the given region.
