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Hello Alicia,
The most straight forward design you can employ here is to simply choose one of your test#.hits files as the reference. You can use the sample with the highest coverage as reference, or a sample that has been used before as reference in other studies, etc. Then you go on comparing all the rest of the chicken samples against this sample and obtain CNV calls relative to this sample. Let's say you choose test1.hits as the reference:
test2.hits vs test1.hits
test3.hits vs test1.hits
test4.hits vs test1.hits
....
Hope it helps,
Rodrigo F.
The most straight forward design you can employ here is to simply choose one of your test#.hits files as the reference. You can use the sample with the highest coverage as reference, or a sample that has been used before as reference in other studies, etc. Then you go on comparing all the rest of the chicken samples against this sample and obtain CNV calls relative to this sample. Let's say you choose test1.hits as the reference:
test2.hits vs test1.hits
test3.hits vs test1.hits
test4.hits vs test1.hits
....
Hope it helps,
Rodrigo F.
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