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+--- Thread: If there are studies with data that hasnt been converted to G25 provide them here (/showthread.php?tid=648)
If there are studies with data that hasnt been converted to G25 provide them here - ilabv - 03-16-2024
There have been many papers without G25 coordinates (recently and perhaps older ones too).
If you know of any studies which dont have G25 coordinates please send me their raw data or at least the study they come from. Teepean has been helping me so I can help the community gong forward
RE: If there are studies with data that hasnt been converted to G25 provide them here - Capsian20 - 03-17-2024
(03-16-2024, 10:30 PM)ilabv Wrote: There have been many papers without G25 coordinates (recently and perhaps older ones too).
If you know of any studies which dont have G25 coordinates please send me their raw data or at least the study they come from. Teepean has been helping me so I can help the community gong forward
I think this last papers without G25 coordinates
RE: If there are studies with data that hasnt been converted to G25 provide them here - pelop - 03-17-2024
(03-16-2024, 10:30 PM)ilabv Wrote: There have been many papers without G25 coordinates (recently and perhaps older ones too).
If you know of any studies which dont have G25 coordinates please send me their raw data or at least the study they come from. Teepean has been helping me so I can help the community gong forward
https://www.sciencedirect.com/science/article/pii/S2589004223022927
https://www.sciencedirect.com/science/article/pii/S2589004223011112
RE: If there are studies with data that hasnt been converted to G25 provide them here - ChrisR - 03-17-2024
Thanks @ilabv and @teepean
See the discussion in the Late Antiquity-Early Middle Ages cemetery in the Eastern Italian Alps thread
Quote:Ancestry and kinship in a Late Antiquity-Early Middle Ages cemetery in the Eastern Italian Alps
https://doi.org/10.1016/j.isci.2023.108215
South Tyrol LA-EMA cemetery of Malles Burgusio Santo Stefano/Mals St. Stephan ob Burgeis (BSS) located in the Venosta/Vinschgau valley
genomes of 21 specimens (shotgun data plus nuclear capture data in four samples)
https://www.ebi.ac.uk/ena/browser/view/PRJEB60362
Maybe the format necessary for submission to Davidski can be created and @Ajeje Brazorf is interested (to get official values)?
RE: If there are studies with data that hasnt been converted to G25 provide them here - Fabrice E - 03-17-2024
I've never seen those, LUN004 and BAL003.
https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1010360
RE: If there are studies with data that hasnt been converted to G25 provide them here - teepean - 03-17-2024
(03-17-2024, 05:31 PM)Fabrice E Wrote: I've never seen those, LUN004 and BAL003.
https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1010360
I created the dataset about a year ago:
https://drive.google.com/drive/folders/1sLTszRuS_cxII6eFemwEORTFoJFXUiJE?usp=sharing
RE: If there are studies with data that hasnt been converted to G25 provide them here - Fabrice E - 03-17-2024
(03-17-2024, 06:08 PM)teepean Wrote:(03-17-2024, 05:31 PM)Fabrice E Wrote: I've never seen those, LUN004 and BAL003.
https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1010360
I created the dataset about a year ago:
https://drive.google.com/drive/folders/1sLTszRuS_cxII6eFemwEORTFoJFXUiJE?usp=sharing
great !
And no one has sent il to David ?
Alright i'll do it
thank you again Teepean
RE: If there are studies with data that hasnt been converted to G25 provide them here - cheshire - 03-18-2024
It's weird we don't have the HGDP Tuscan samples included in the dataset yet. It's always been on gedmatch and I thought HGDP data was easily obtainable? They're used by Li et al., Science (2008).
Unfortunately I don't have a clue on how or where to download them but the samples are as follows:
HGDP01161
HGDP01162
HGDP01163
HGDP01164
HGDP01167
HGDP01168
HGDP01169
RE: If there are studies with data that hasnt been converted to G25 provide them here - Kale - 03-18-2024
How about this one? Red Deer Cave
https://www.cell.com/current-biology/fulltext/S0960-9822(22)00928-9
RE: If there are studies with data that hasnt been converted to G25 provide them here - ilabv - 03-18-2024
Thanks everyone, keep sending them and I'll get to every single one when I can
RE: If there are studies with data that hasnt been converted to G25 provide them here - Fabrice E - 03-18-2024
(03-17-2024, 06:08 PM)teepean Wrote:(03-17-2024, 05:31 PM)Fabrice E Wrote: I've never seen those, LUN004 and BAL003.
https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1010360
I created the dataset about a year ago:
https://drive.google.com/drive/folders/1sLTszRuS_cxII6eFemwEORTFoJFXUiJE?usp=sharing
Unfortunately, not enough data for the G25
RE: If there are studies with data that hasnt been converted to G25 provide them here - ilabv - 03-18-2024
(03-18-2024, 06:24 AM)Fabrice E Wrote:(03-17-2024, 06:08 PM)teepean Wrote:(03-17-2024, 05:31 PM)Fabrice E Wrote: I've never seen those, LUN004 and BAL003.
https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1010360
I created the dataset about a year ago:
https://drive.google.com/drive/folders/1sLTszRuS_cxII6eFemwEORTFoJFXUiJE?usp=sharing
Unfortunately, not enough data for the G25
That is weird, they are 2.4x and 16.5x coverage
RE: If there are studies with data that hasnt been converted to G25 provide them here - ilabv - 03-18-2024
4 new samples from this study: https://www.nature.com/articles/s41598-023-45612-3
Scaled
BellBeaker:ALW1,0.121791,0.116786,0.055814,0.068476,0.035391,0.025658,0.00329,0.003692,0.001227,-0.010387,-0.005359,0.005545,-0.013528,-0.018166,0.02538,0.017237,0.008736,0.003801,0.004777,0.018009,0.005615,0.009769,-0.003204,-0.000602,-0.001197
BellBeaker:ALW2,0.124067,0.116786,0.063356,0.067507,0.033545,0.026216,0.005405,0.004154,-0.005318,-0.01713,-0.010555,-0.002098,-0.008028,-0.026424,0.022665,0.016971,0.009909,0.00076,-0.001006,0.016633,0.007986,0.006306,-0.001479,0.003976,0.000838
BellBeaker:LUT1,0.117238,0.135065,0.070144,0.05491,0.038776,0.019522,0.00235,0.002769,-0.001432,-0.004191,-0.004709,0.002548,-0.011596,-0.011423,0.023615,-0.003447,-0.024121,0.001267,0.002388,0,0.007736,0.006925,0.000863,0.003976,-0.008263
BellBeaker:LUT2,0.122929,0.133034,0.058831,0.050065,0.035391,0.023427,0.00282,0.002308,0.002863,0.005285,-0.005846,0.002098,-0.012785,-0.01968,0.019815,0.011138,-0.002868,0.004561,0.006788,-0.00025,0.010981,0.001978,-0.002218,0.001928,-0.003473
Raw
BellBeaker:ALW1,0.0107,0.0115,0.0148,0.0212,0.0115,0.0092,0.0014,0.0016,0.0006,-0.0057,-0.0033,0.0037,-0.0091,-0.0132,0.0187,0.013,0.0067,0.003,0.0038,0.0144,0.0045,0.0079,-0.0026,-0.0005,-0.001
BellBeaker:ALW2,0.0109,0.0115,0.0168,0.0209,0.0109,0.0094,0.0023,0.0018,-0.0026,-0.0094,-0.0065,-0.0014,-0.0054,-0.0192,0.0167,0.0128,0.0076,0.0006,-0.0008,0.0133,0.0064,0.0051,-0.0012,0.0033,0.0007
BellBeaker:LUT1,0.0103,0.0133,0.0186,0.017,0.0126,0.007,0.001,0.0012,-0.0007,-0.0023,-0.0029,0.0017,-0.0078,-0.0083,0.0174,-0.0026,-0.0185,0.001,0.0019,0,0.0062,0.0056,0.0007,0.0033,-0.0069
BellBeaker:LUT2,0.0108,0.0131,0.0156,0.0155,0.0115,0.0084,0.0012,0.001,0.0014,0.0029,-0.0036,0.0014,-0.0086,-0.0143,0.0146,0.0084,-0.0022,0.0036,0.0054,-0.0002,0.0088,0.0016,-0.0018,0.0016,-0.0029
RE: If there are studies with data that hasnt been converted to G25 provide them here - ilabv - 03-18-2024
(03-18-2024, 05:03 AM)Kale Wrote: How about this one? Red Deer Cave
https://www.cell.com/current-biology/fulltext/S0960-9822(22)00928-9
I couldn't find the raw data for this one. It takes me to a dead link:
https://ngdc.cncb.ac.cn/gsa-human/browse/HRA002402
RE: If there are studies with data that hasnt been converted to G25 provide them here - Norfern-Ostrobothnian - 03-18-2024
(03-18-2024, 05:03 AM)Kale Wrote: How about this one? Red Deer Cave
https://www.cell.com/current-biology/fulltext/S0960-9822(22)00928-9
I checked that once, the SNP count was pitiful
And going through the Chinese database was awful too.