I load in Galaxy server about 10 histories. Each one is composed of a fastq file and the related intercepts with known genome sequences of my interest (Alu sequences).
Now I would like to compare the samples (histories) considering the regions of my interest and so by quantifying the number of regions per library and the positions of the regions in the genome.
I would expect that a disease genotype is characterized by a different position of the Alu sequences along the genome.
Thank you Francesco