Add 2023_VillaIslas_Science #18
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4 tasks
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@93Boy do you think you could make a start with this? |
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New situation: We now have a Janno file PR in the PCA. Thiseas can pull from there. Nothing to do here, @93Boy |
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Update: @KenanaSa99 and @Kavlahkaff have started looking into it. |
merged janno from community archive for 2023_VillaIslas_Science
… file. Add @Kavlahkaff, @jbv2 as Contributors.
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Facing the same issue as #27 |
TCLamnidis
added
the
Final review needed
nevrome
reviewed
Jan 2, 2025
| Ranas 37AI_R_b_MNT Ranas 0 0 0 | ||
| Toluquilla 6428A_TOL_b_MNT Toluquilla 0 1 0 | ||
| Ranas 7A_R_b_MNT Ranas 0 1 0 | ||
| CañadadelaVirgen E10_CdV_b_MNT CañadadelaVirgen 0 0 0 |
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As already discussed elsewhere I think we should avoid non-ASCII characters in individual and primary group IDs.
| 333C_TOL_a_MNT F Toluquilla;CentralMexico;SierraGorda Mexico MX Querétaro Toluquilla 20.88378 -99.53097 contextual 1301 1351 1401 Dates are taken from Date (CE) in S15 B2c n/a tooth 1 mtDNA-genome Shotgun minus ds haploid https://github.com/nf-core/eager/releases/tag/2.4.6 94.499718 0 0.21912157243387528 n/a n/a n/a Nr Snps (per library): 0. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded. PRJEB51440;ERS10903723;ERR9576915 2023VillaIslasScience 333C_TOL_a 333C_TOL_a 0.0 0.0 0.0 0.0 | ||
| 333O_TOL_b_MNT U Toluquilla;CentralMexico;SierraGorda Mexico MX Querétaro Toluquilla 20.88378 -99.53097 contextual 650 700 750 Dates are taken from Date (CE) in S5 B2l n/a tooth 1 mtDNA-genome Shotgun minus ds haploid https://github.com/nf-core/eager/releases/tag/2.4.6 97.512945 0 0.31377645748236166 n/a n/a n/a Nr Snps (per library): 0. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded. PRJEB51440;ERS10903713;ERR9576916 2023VillaIslasScience 333O_TOL_b 333O_TOL_b 0.0 0.0 0.0 0.0 | ||
| 333Q_TOL_b_MNT U Toluquilla;CentralMexico;SierraGorda Mexico MX Querétaro Toluquilla 20.88378 -99.53097 contextual 480 520 560 Dates are taken from Date (CE) in S10 A2d n/a tooth 1 mtDNA-genome Shotgun minus ds haploid https://github.com/nf-core/eager/releases/tag/2.4.6 98.044843 0 0.20524344569288389 n/a n/a n/a Nr Snps (per library): 0. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded. PRJEB51440;ERS10903718;ERR9576917 2023VillaIslasScience 333Q_TOL_b 333Q_TOL_b 0.0 0.0 0.0 0.0 | ||
| 37AI_R_b_MNT U Ranas;CentralMexico;SierraGorda Mexico MX Querétaro Ranas 20.92612 -99.56488 n/a n/a n/a n/a Dates are taken from Date (CE) in S9 A2d n/a tooth 1 mtDNA-genome Shotgun minus ds haploid https://github.com/nf-core/eager/releases/tag/2.4.6 96.207416 0 0.3249466950959488 n/a n/a n/a Nr Snps (per library): 0. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded. PRJEB51440;ERS10903717;ERR9576918 2023VillaIslasScience 37AI_R_b 37AI_R_b 0.0 0.0 0.0 0.0 |
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Date_Note says "Dates are taken from Date (CE) in S9", but there is no date information. This also applies to some other samples here. What does "S9" mean, btw.?
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| Poseidon_ID Genetic_Sex Group_Name Country Country_ISO Location Site Latitude Longitude Date_Type Date_BC_AD_Start Date_BC_AD_Median Date_BC_AD_Stop Date_Note MT_Haplogroup Y_Haplogroup Source_Tissue Nr_Libraries Library_Names Capture_Type UDG Library_Built Genotype_Ploidy Data_Preparation_Pipeline_URL Endogenous Nr_SNPs Damage Contamination Contamination_Err Contamination_Meas Contamination_Note Genetic_Source_Accession_IDs Publication Eager_ID Main_ID RateErrX RateErrY RateX RateY | |||
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I think the Library_Names column is filled incorrectly. It should include "identifiers of the libraries used to generate the genotype data for the sample", but here it has entries like "mtDNA-genome;Whole-genome". These are not library IDs. What does that mean here?
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| Poseidon_ID Genetic_Sex Group_Name Country Country_ISO Location Site Latitude Longitude Date_Type Date_BC_AD_Start Date_BC_AD_Median Date_BC_AD_Stop Date_Note MT_Haplogroup Y_Haplogroup Source_Tissue Nr_Libraries Library_Names Capture_Type UDG Library_Built Genotype_Ploidy Data_Preparation_Pipeline_URL Endogenous Nr_SNPs Damage Contamination Contamination_Err Contamination_Meas Contamination_Note Genetic_Source_Accession_IDs Publication Eager_ID Main_ID RateErrX RateErrY RateX RateY | |||
| 11R_R_b_MNT M Ranas;CentralMexico;SierraGorda Mexico MX Querétaro Ranas 20.92612 -99.56488 contextual 729 769 809 Dates are taken from Date (CE) in S6 D1m Q1a2a1-L54 tooth 2 mtDNA-genome;Whole-genome Shotgun minus ds haploid https://github.com/nf-core/eager/releases/tag/2.4.6 99.296225 8454 0.25554637284974846 n/a n/a n/a Nr Snps (per library): 0;0. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded. PRJEB51440;ERS10903714;ERR9576909;ERR9169797 2023VillaIslasScience 11R_R_b 11R_R_b 0.033425961437661 0.056720746903437 0.389404695593133 0.73410877311746 | |||
| 2417C_TOL_a_MNT F Toluquilla;CentralMexico;SierraGorda Mexico MX Querétaro Toluquilla 20.88378 -99.53097 contextual 1100 1160 1220 Dates are taken from Date (CE) in S11 A2d n/a tooth 1 mtDNA-genome Shotgun minus ds haploid https://github.com/nf-core/eager/releases/tag/2.4.6 98.932551 0 0.3336998350742166 n/a n/a n/a Nr Snps (per library): 0. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded. PRJEB51440;ERS10903719;ERR9576910 2023VillaIslasScience 2417C_TOL_a 2417C_TOL_a 0.0 0.0 0.0 0.0 | |||
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Aha - I got the misplaced info in the Library_Names column now. So for this and other samples only mtDNA was sequenced. As a consequence the number of covered SNPs is zero. I guess it was a conscious decision to include these samples anyway in the Poseidon package, right?
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Adds package
2023_VillaIslas_Science.Linked to poseidon-framework/minotaur-recipes#3
Publication is missing from the community archive, so metadata needs to be collected manually.
Janno for publication provided by @jbv2 here, and added by @Kavlahkaff