3 ms·
It's a bit frustrating (and concerning?) that their data repository [1] seems incomplete; the most important seqences (GM12878 / HG001) are missing from everyt
by zmmmmm 7y ago
It's a bit frustrating (and concerning?) that their data repository [1] seems incomplete; the most important seqences (GM12878 / HG001) are missing from everything but the raw data directory. This is the sample that most laboratories would likely have readily available for comparison to their results, but for some reason they have omitted to deposit their final results for it (unless I'm missing something ...).
[1] https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix= https://s3-us-west-2.amazonaws.com/human-pangenomics/index.h...
- vikramkr 7y agoIs it in any of the supplementary information or in any of the figure source data links in the paper? They do link in addition to the AWS open data this link (https://www.ebi.ac.uk/ena/data/search?query=PRJEB37264 https://www.ebi.ac.uk/ena/data/search?query=PRJEB37264) - did you look through that? Other than that now idea - seems like a bit of an oversight from nature if they wouldn't make sure important sequences were readily available, you'd imagine they'd be important for peer review as well prior to publication.
- terrakota 7y agoLook at their "sample selection" section. "The goal of sample selection was to select a set of individuals that collectively captured the maximum amount of weighted allelic diversity53." And also says "We also added the three Ashkenazim Trio samples and the Puerto Rican individual (HG00733). These four samples were added for the purposes of comparison with other studies that are using them." Four genomes make a comprehensive evaluation set, don't think HG001 is "absolutely" needed.