200001 300001 322 0 0.0186335 100 100 0.830329 -2.4124
300001 400001 2580 0 0.0124031 100 100 1.58813 -2.50684
400001 500001 2452 0 0.0146819 100 100 1.07317 -2.37506
500001 600001 2671 0 0.00112317 100 100 1.36972 -2.37935
600001 700001 3260 0 0.0107362 100 100 0.911084 -2.55303
700001 800001 2577 0 0.096624 100 5 1.17995 -2.65801
800001 900001 2848 0 0.00702247 100 100 1.71611 -2.50936
900001 1000001 2555 0 0.0172211 100 100 0.905464 -2.44362
1000001 1100001 2622 0 0.011823 100 100 0.753539 -2.87985
1100001 1200001 2145 0 0.0494172 100 100 1.00829 -2.49665
1200001 1300001 2739 0 0.0277474 100 100 1.9245 -2.68171
Hello!
I am currently performing XPEHH analysis on chromosomes 1–22 in the CHB population and aim to generate a genome-wide Manhattan plot to identify candidate regions under positive selection. However, I am unsure which column of the output data should be used for plotting the Manhattan plot.
In a paper I previously read, the authors used the values from the eighth column—specifically, the maximum value within each window—to represent that window and construct the Manhattan plot. I was wondering if you have any recommendations regarding this. Which column is typically used for generating Manhattan plots in XPEHH analyses?
Additionally, after completing the genome-wide XPEHH analysis, I would like to examine the XPEHH values at individual sites within a specific region of interest (for example, chr11:130000–150000). In this case, should I directly extract the relevant data from the genome-wide results, or would it be more appropriate to rerun selscan focusing only on this region and its surrounding areas? I find this aspect somewhat confusing and would greatly appreciate your guidance.
Thank you very much for your time and assistance.
200001 300001 322 0 0.0186335 100 100 0.830329 -2.4124
300001 400001 2580 0 0.0124031 100 100 1.58813 -2.50684
400001 500001 2452 0 0.0146819 100 100 1.07317 -2.37506
500001 600001 2671 0 0.00112317 100 100 1.36972 -2.37935
600001 700001 3260 0 0.0107362 100 100 0.911084 -2.55303
700001 800001 2577 0 0.096624 100 5 1.17995 -2.65801
800001 900001 2848 0 0.00702247 100 100 1.71611 -2.50936
900001 1000001 2555 0 0.0172211 100 100 0.905464 -2.44362
1000001 1100001 2622 0 0.011823 100 100 0.753539 -2.87985
1100001 1200001 2145 0 0.0494172 100 100 1.00829 -2.49665
1200001 1300001 2739 0 0.0277474 100 100 1.9245 -2.68171
Hello!
I am currently performing XPEHH analysis on chromosomes 1–22 in the CHB population and aim to generate a genome-wide Manhattan plot to identify candidate regions under positive selection. However, I am unsure which column of the output data should be used for plotting the Manhattan plot.
In a paper I previously read, the authors used the values from the eighth column—specifically, the maximum value within each window—to represent that window and construct the Manhattan plot. I was wondering if you have any recommendations regarding this. Which column is typically used for generating Manhattan plots in XPEHH analyses?
Additionally, after completing the genome-wide XPEHH analysis, I would like to examine the XPEHH values at individual sites within a specific region of interest (for example, chr11:130000–150000). In this case, should I directly extract the relevant data from the genome-wide results, or would it be more appropriate to rerun selscan focusing only on this region and its surrounding areas? I find this aspect somewhat confusing and would greatly appreciate your guidance.
Thank you very much for your time and assistance.