I've been trying to do basic eQTL detection between the expression profiles located at http://resource.psychencode.org/ (DER-02_PEC_Gene_expression_matrix_TPM), and the Capstone genotypes. However, there are a few hundred individuals in the expression matrix that I cannot find corresponding genotypes (or clinical or metadata for) in the Capstone data. Below are some examples of those IDs, how can I figure out which individuals they are in the Capstone data? Thanks! Br1413 Br1601 Br1395 Br871 Br1309 Br1470 Br1423 Br1838 Br931 Br1724 Br1415 Br1630 Br1450 Br1969 Br2013 Br2035 Br2042 Br1751 Br1505 Br1690 Br2001 Br2027 Br1729 Br1529 Br2298 Br1667 Br2039 Br891 Br1269 Br2371 Br1399 Br2295 Br1646 Br1578 Br1637 Br856 Br873 Br1431 Br1851 Br1531 Br1706 Br1548 Br1539 Br1380 Br1424 Br1281 Br1250 Br1657 Br1443 Br1342 Br1405 Br1581 Br1965 Br959 Br1385 Br1878 Br1847 Br1556 Br1868 Br1193 Br1227 Br2052 Br1412 Br1331 Br1263 Br1571 Br1975 Br1861 Br1560 Br1872 Br1880 Br1611 Br1856 Br1859 Br1853 Br1961 Br1512 Br1875 Br1691 Br1854 Br1563 Br1494 Br1674 Br1615 Br1670 Br1855 Br1654 Br1860 Br1874 Br1866 Br973 Br826 Br863 Br993 Br822 Br898 Br1054 Br831 Br890 Br836 Br845 Br991 Br1003 Br848 Br1069 Br852 Br1378 Br1061 Br1613 Br1848 Br1058 Br1039 Br1006 Br1033 Br887 Br982 Br1881 Br926 Br1096 Br2294 Br2427 Br2309 Br2065 Br2364 Br1652 Br2444 Br2328 Br2379 Br2078 Br2272 Br1160 Br1474 Br1644 Br1148 Br1985 Br1836 Br1877 Br1187 Br1185 Br1565 Br1604 Br1518 Br1722 Br1137 Br1107 Br1150 Br1697 Br894 Br1111 Br924 Br1964 Br1558 Br1469 Br1133 Br1164 Br2573 Br2351 Br2605 Br2543 Br2301 Br2297 Br2652 Br2322 Br2345 Br2557 Br2348 Br2653 Br2333 Br2337 Br2476 Br2474 Br2346 Br2641 Br2321 Br2582 Br2655 Br2454 Br2405 Br2521 Br2589 Br2574 Br2542 Br2539 Br2607 Br2585 Br2520 Br2534 Br2532 Br2513 Br2636 Br2541 Br2538 Br2623 Br2612 Br2572 Br2509 Br2595 Br2569 Br2588 Br2530 Br2470 Br2421 Br2626 Br2423 Br2469 Br2477 Br2353 Br2377 Br2448 Br2355 Br2580 Br2429 Br2305 Br2591 Br2622 Br2587 Br1435 Br1490 Br2266 Br1434 Br977 Br839 Br1287

Created by Gerald Quon geraldquon
Hi @josie.gleeson and @geraldquon - We posted a file, **Phase I Capstone Collection Data Map**, in syn21978133 containing these mappings. Please let us know if you run into additional issues.
The resource.psychencode used BrXXX individual IDs for CMC_HBCC individuals, whereas the PsychENCODE database on Synapse uses CMC_HBCC_XX . Agreed, having the sample IDs would allow us to cross-match them.
Hello, did you end up solving this? I am having the same issue... thanks.
@Mette One thing that would help is if there was a file that described how the sample IDs in DER-02 (http://resource.psychencode.org/ (DER-02_PEC_Gene_expression_matrix_TPM) map to the sample IDs in the Synapse Capstone data, because not all of them match -- -do you happen to know where I can find this mapping? Thanks!
@Mette Hi Mette, can you help me on this? We're still not able to find these individuals. From just the combination of CMC/CMC_HBCC datasets, using the Capstone data, I can only get ~600 samples with genotype, expression and clinical covariate data, but when I access the (non-Capstone) CMC/CMC_HBCC directly, I can map ~930+ samples. However, I want to use the Capstone expression data here (http://resource.psychencode.org/ (DER-02_PEC_Gene_expression_matrix_TPM). How do I get a complete mapping of IDs from the DER-02 expression data to the genotype/clinical covariate data stored on Synapse? Thanks!

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