Entering edit mode
7.9 years ago
beausoleilmo
▴
600
I was wondering if Scaffolds could overlap and why.
Here is a table showing my scaffolds (Under CHR). The minPos is the minimum position of a SNP in that Scaffold and maxPos is the same thing but for the maximum. I thought that the SNPs would be positioned in non overlapping scaffolds, but now I don't understand why some of the scaffolds are overlapping.
CHR minPos maxPos
1 739908 809 8420455
2 739893 981 16982050
3 740134 1196 806099
4 739934 2164 5673875
5 740027 3038 1882819
6 739900 3652 12059715
7 740035 5243 1752428
8 739891 5666 19027684
9 740062 5748 1391297
10 739970 8065 3377070
11 740050 12528 1511536
12 739951 16014 4263239
13 739890 16652 19779756
In this image, you can see that scaffolds are not overlapping. Is this a misconception of the scaffolds?
I'm not really clear on your question. The diagram clearly indicates that contigs do not overlap (which is correct), and indicates that multiple contigs can be placed on the same scaffold (which is also correct). But I don't understand how this relates to the data you posted. Can you explain the meaning of the columns? You only have 3 labels for 4 columns, and it is not at all clear what any of the headers mean.
I finally understood that a scaffold is always starting at position 1. So scaffold1 starts at 1 and ends at 500 for example. Scaffold2 could start at 1 and end at 340. I thought they were positioned relative to the "real" physical position on the genome.