[R-sig-Geo] advice needed on genomic question

[João Fadista]

Dear all,
 
I am new member of this mailing list and I would like some advice of what should I do with my data. Maybe it´s a wild guess but I just thought that spatial statistics can help me. Here it goes:
 
I am analysing data from whole genome shotgun (WGS) sequencing of the cow and I am comparing the obtained numerous small sequences to the cow reference genome assembly. The WGS sequences are from a cow breed but the reference genome is from another breed. I mapped the obtained sequences to the reference genome with an algorithm similar to BLAST and now I have an output file with the score (-> like a probability) of the alignment for each of my WGS sequences. 
In attachment there is a picture with the genome reference sequence and my WGS sequences (called "tag" with light blue color) and the correspondent scores. In this picture we just see a small portion of the chromosome 1 of the cow genome.
 
Therefore, I would like to know if it is possible to use some R packages that deal with spatial analysis in order to see if there is any region of the genome that is statistically more dense in these tags than another region. 
 
Thanks for you time.
 


Best regards

João Fadista
Ph.d. student


 	
 	 UNIVERSITY OF AARHUS	
Faculty of Agricultural Sciences	
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E-mail:	 Joao.Fadista at agrsci.dk <mailto:Joao.Fadista at agrsci.dk> 	
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