Add Details to qMotif Documentation

[DarioS]

It would be nice to know how to create the configuration for another genome, such as hg38 or mouse genome. The example is:

; name, regions (sequence:start-stop)
chr1p   chr1:10001-12464
chr1q   chr1:249237907-249240620
chr2p   chr2:10001-12592
chr2q   chr2:243187373-243189372
chr2xA  chr2:243150480-243154648
chr3p   chr3:60001-62000
chr3q   chr3:197960430-197962429

but, when I use UCSC Genome Browser's Table Browser and extract telomeres from the Gap table, I got different coordinates.

#filter: gap.type like '%telo%'
#chrom	chromStart	chromEnd	type
chr1	0	10000	telomere
chr1	249240621	249250621	telomere
chr2	0	10000	telomere
chr2	243189373	243199373	telomere
chr3	0	10000	telomere
chr3	198012430	198022430	telomere

I used hg19 for direct comparison. How should the coordinates in the configuration file be correctly derived? The regions that qMotif uses seems to be adjacent to the ones I get from Table Browser, but I don't understand what the difference is.

Also, the section which describes the XML file does not give an example of how to correctly interpret it. How should the user determine the telomere length from the various numbers in the XML file?