avilella
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Posts: 35
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Hi,
I am running the F_ST.bf module for some hapmap genotypes, but I don't know how to define my populations.
given this ids:
Read the following data:218 species:{CEPH1334.01_1,CEPH1334.01_2,CEPH1334.02_1,CEPH1334.02_2,CEPH1334.11_1,C EPH1334.11_2,CEPH1334.12_1,CEPH1334.12_2,CEPH1334.13_1,CEPH1334.13_2,CEPH1340.01 _1,CEPH1340.01_2,CEPH1340.10_1,CEPH1340.10_2,CEPH1340.11_1,CEPH1340.11_2,CEPH134 0.12_1,CEPH1340.12_2,CEPH1341.01_1,CEPH1341.01_2,CEPH1341.02_1,CEPH1341.02_2,CEP H1341.11_1,CEPH1341.11_2,CEPH1341.12_1,CEPH1341.12_2,CEPH1341.13_1,CEPH1341.13_2 ,CEPH1344.12_1,CEPH1344.12_2,CEPH1344.13_1,CEPH1344.13_2,CEPH1345.13_1,CEPH1345. 13_2,CEPH1346.11_1,CEPH1346.11_2,CEPH1346.12_1,CEPH1346.12_2,CEPH1347.02_1,CEPH1 347.02_2,CEPH1347.15_1,CEPH1347.15_2,CEPH1349.13_1,CEPH1349.13_2,CEPH1349.14_1,C EPH1349.14_2,CEPH1350.02_1,CEPH1350.02_2,CEPH1350.10_1,CEPH1350.10_2,CEPH1350.11 _1,CEPH1350.11_2,CEPH1350.12_1,CEPH1350.12_2,CEPH1350.13_1,CEPH1350.13_2,CEPH135 8.01_1,CEPH1358.01_2,CEPH1358.11_1,CEPH1358.11_2,CEPH1358.12_1,CEPH1358.12_2,CEP H1362.13_1,CEPH1362.13_2,CEPH1362.14_1,CEPH1362.14_2,CEPH1362.15_1,CEPH1362.15_2 ,CEPH1362.16_1,CEPH1362.16_2,CEPH1375.02_1,CEPH1375.02_2,CEPH1375.11_1,CEPH1375. 11_2,CEPH1375.12_1,CEPH1375.12_2,CEPH1408.10_1,CEPH1408.10_2,CEPH1408.12_1,CEPH1 408.12_2,CEPH1408.13_1,CEPH1408.13_2,CEPH1416.11_1,CEPH1416.11_2,CEPH1416.12_1,C EPH1416.12_2,CEPH1420.01_1,CEPH1420.01_2,CEPH1420.02_1,CEPH1420.02_2,CEPH1420.09 _1,CEPH1420.09_2,CEPH1420.11_1,CEPH1420.11_2,CEPH1444.02_1,CEPH1444.02_2,CEPH144 7.01_1,CEPH1447.01_2,CEPH1447.02_1,CEPH1447.02_2,CEPH1447.11_1,CEPH1447.11_2,CEP H1447.12_1,CEPH1447.12_2,CEPH1454.01_1,CEPH1454.01_2,CEPH1454.02_1,CEPH1454.02_2 ,CEPH1454.12_1,CEPH1454.12_2,CEPH1454.15_1,CEPH1454.15_2,CEPH1459.01_1,CEPH1459. 01_2,CEPH1459.02_1,CEPH1459.02_2,CEPH1459.09_1,CEPH1459.09_2,CEPH1459.10_1,CEPH1 459.10_2,CEPH1459.11_1,CEPH1459.11_2,CEPH1459.12_1,CEPH1459.12_2,CEPH1463.02_1,C EPH1463.02_2,CEPH1463.15_1,CEPH1463.15_2,CEPH1463.16_1,CEPH1463.16_2,CH18524_1,C H18524_2,CH18526_1,CH18526_2,CH18529_1,CH18529_2,CH18532_1,CH18532_2,CH18537_1,C H18537_2,CH18540_1,CH18540_2,CH18542_1,CH18542_2,CH18545_1,CH18545_2,CH18547_1,C H18547_2,CH18550_1,CH18550_2,CH18552_1,CH18552_2,CH18555_1,CH18555_2,CH18558_1,C H18558_2,CH18561_1,CH18561_2,CH18562_1,CH18562_2,CH18563_1,CH18563_2,CH18564_1,C H18564_2,CH18566_1,CH18566_2,CH18570_1,CH18570_2,CH18571_1,CH18571_2,CH18572_1,C H18572_2,CH18573_1,CH18573_2,CH18576_1,CH18576_2,CH18577_1,CH18577_2,CH18579_1,C H18579_2,CH18592_1,CH18592_2,CH18593_1,CH18593_2,CH18594_1,CH18594_2,CH18603_1,C H18603_2,CH18605_1,CH18605_2,CH18608_1,CH18608_2,CH18609_1,CH18609_2,CH18611_1,C H18611_2,CH18612_1,CH18612_2,CH18620_1,CH18620_2,CH18621_1,CH18621_2,CH18622_1,C H18622_2,CH18623_1,CH18623_2,CH18624_1,CH18624_2,CH18632_1,CH18632_2,CH18633_1,C H18633_2,CH18635_1,CH18635_2,CH18636_1,CH18636_2,CH18637_1,CH18637_2}; Total Sites:66; Distinct Sites:5
I would like to define a clade for "CEPH*" and another one for "CH*", but it doesn't seem to work if I use "CEPH" and "CH":
Clade 1 includes 118 sequences: CEPH1334.01_1 CEPH1334.01_2 CEPH1334.02_1 CEPH1334.02_2 CEPH1334.11_1 CEPH1334.11_2 CEPH1334.12_1 CEPH1334.12_2 CEPH1334.13_1 CEPH1334.13_2 CEPH1340.01_1 CEPH1340.01_2 CEPH1340.10_1 CEPH1340.10_2 CEPH1340.11_1 CEPH1340.11_2 CEPH1340.12_1 CEPH1340.12_2 CEPH1341.01_1 CEPH1341.01_2 CEPH1341.02_1 CEPH1341.02_2 CEPH1341.11_1 CEPH1341.11_2 CEPH1341.12_1 CEPH1341.12_2 CEPH1341.13_1 CEPH1341.13_2 CEPH1344.12_1 CEPH1344.12_2 CEPH1344.13_1 CEPH1344.13_2 CEPH1345.13_1 CEPH1345.13_2 CEPH1346.11_1 CEPH1346.11_2 CEPH1346.12_1 CEPH1346.12_2 CEPH1347.02_1 CEPH1347.02_2 CEPH1347.15_1 CEPH1347.15_2 CEPH1349.13_1 CEPH1349.13_2 CEPH1349.14_1 CEPH1349.14_2 CEPH1362.14_1 CEPH1362.14_2 CEPH1408.10_1 CEPH1408.10_2 CEPH1408.12_1 CEPH1408.12_2 CEPH1408.13_1 CEPH1408.13_2 CEPH1416.11_1 CEPH1416.11_2 CEPH1416.12_1 CEPH1416.12_2 CEPH1420.01_1 CEPH1420.01_2 CEPH1420.02_1 CEPH1420.02_2 CEPH1420.09_1 CEPH1420.09_2 CEPH1420.11_1 CEPH1420.11_2 CEPH1444.02_1 CEPH1444.02_2 CEPH1447.01_1 CEPH1447.01_2 CEPH1447.02_1 CEPH1447.02_2 CEPH1447.11_1 CEPH1447.11_2 CEPH1447.12_1 CEPH1447.12_2 CEPH1454.01_1 CEPH1454.01_2 CEPH1454.02_1 CEPH1454.02_2 CEPH1454.12_1 CEPH1454.12_2 CEPH1454.15_1 CEPH1454.15_2 CEPH1459.01_1 CEPH1459.01_2 CEPH1459.02_1 CEPH1459.02_2 CEPH1459.09_1 CEPH1459.09_2 CEPH1459.10_1 CEPH1459.10_2 CEPH1459.11_1 CEPH1459.11_2 CEPH1459.12_1 CEPH1459.12_2 CEPH1463.02_1 CEPH1463.02_2 CEPH1463.15_1 CEPH1463.15_2 CEPH1463.16_1 CEPH1463.16_2 CH18524_1 CH18524_2 CH18540_1 CH18540_2 CH18542_1 CH18542_2 CH18545_1 CH18545_2 CH18547_1 CH18547_2 [...]
Clade 2 includes 28 sequences: CEPH1350.02_1 CEPH1350.02_2 CEPH1350.10_1 CEPH1350.10_2 CEPH1350.11_1 CEPH1350.11_2 CEPH1350.12_1 CEPH1350.12_2 CEPH1350.13_1 CEPH1350.13_2 CEPH1358.01_1 CEPH1358.01_2 CEPH1358.11_1 CEPH1358.11_2 CEPH1358.12_1 CEPH1358.12_2 CEPH1362.13_1 CEPH1362.13_2 CEPH1362.15_1 CEPH1362.15_2 CEPH1362.16_1 CEPH1362.16_2 CEPH1375.02_1 CEPH1375.02_2 CEPH1375.11_1 CEPH1375.11_2 CEPH1375.12_1 CEPH1375.12_2
Is this partitioning correct (y/n) Proportion of sequence in population 1: 0.808219 Proportion of sequence in population 2: 0.191781
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How does the regexp bit work?
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