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When a package is modified in any way (e.g. updates of the context information in the `.janno` file), then the `packageVersion` field should be incremented and the `lastModified` field updated to the current date.
@@ -125,7 +129,7 @@ Example:
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}
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```
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## The `README.txt` file
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## The `README.md` file
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Informal information accompanying the package.
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This package contains a rather interesting set of samples relevant for the peopling of the Territory of Christmas Island in the Indian Ocean. We consider this especially relevant, because ...
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```
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## The `CHANGELOG.txt` file
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## The `CHANGELOG.md` file
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Documentation of important changes in the history of a package.
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Example:
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```
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V 1.2.0: Fixed a spelling mistake in the site name "Hosenacker"->"Rosenacker"
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V 1.1.1: Added mtDNA contamination estimation to .janno file
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V 1.1.0: The authors of @Gassenhauer_2021 made some previously restricted samples for their publication available later and we added them
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V 1.0.0: Creation of the package
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- V 1.2.0: Fixed a spelling mistake in the site name "Hosenacker"->"Rosenacker"
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- V 1.1.1: Added mtDNA contamination estimation to .janno file
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- V 1.1.0: The authors of @Gassenhauer_2021 made some previously restricted samples for their publication available later and we added them
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- V 1.0.0: Creation of the package
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```
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## The Sequencing Source file
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## The `.ssf` file
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Poseidon 2.7.0 added an option to specify sequencing source data. This is a tab-separated table, much like the `.janno` file, but following a different schema, specified in the file `ssf_columns.tsv`.
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Note that the primary entities in this table are sequencing entities (typically corresponding to DNA libraries or even multiple runs/lanes of the same library). The link to the Individuals listed in the `.janno`-file are made through a foreign-key relationship into `Poseidon_ID`.
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Poseidon 2.7.0 added an option to specify sequencing source data. This is a tab-separated table, much like the Janno file, but following a different schema, specified in the file `sequencingSourceFile_columns.tsv`. Note that the primary entities in this table are Sequencing entities (typically corresponding to DNA libraries or even multiple runs/lanes of the same library). The link to the Individuals listed in the Janno-file are made through a foreign-key relationship into `Poseidon_ID`.
Copy file name to clipboardExpand all lines: janno_columns.tsv
+5-3Lines changed: 5 additions & 3 deletions
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@@ -9,6 +9,7 @@ Relation_Type relationship type for relatives mentioned in Related_To as an arbi
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Relation_Notearbitrary comments about the relations of this individualStringFALSEFALSEFALSEFALSEFALSE
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Collection_IDid as defined by the provider/owner of a sample (e.g. grave 40 skeleton 2)StringFALSEFALSEFALSEFALSEFALSE
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Countrypresent-day political countryStringFALSEFALSEFALSEFALSEFALSE
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Country_ISOpresent-day political country expressed in ISO 3166-1 alpha-2 country codesStringFALSEFALSEFALSEFALSEFALSE
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Locationunspecified location information like administrative or topographic region or mountains/rivers/lakes/cities nearbyStringFALSEFALSEFALSEFALSEFALSE
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Sitesite nameStringFALSEFALSEFALSEFALSEFALSE
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Latitudelatitude with up to 5 places after the decimal pointFloatFALSEFALSETRUE-9090FALSEFALSE
@@ -23,11 +24,12 @@ Date_BC_AD_Stop upper (more recent) bound for the age, negative numbers for BC,
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Date_Notea free text field for arbitrary comments about the dating informationStringFALSEFALSEFALSEFALSEFALSE
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MT_Haplogroupmitochondrial haplogroup after phylotree.org as reported by Haplofind or HaplogrepStringFALSEFALSEFALSEFALSEFALSE
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Y_HaplogroupY-chromosome haplogroup reported as published, for internal data, please follow syntax with main branch + most terminal derived Y-SNP (e.g. R1b-P312)StringFALSEFALSEFALSEFALSEFALSE
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Source_Tissueskeletal/tissue/source elements, specific bone name should be reported with an underscore (e.g. bone_phalanx), multiple values separated by ; in case of multiple librariesStringTRUEFALSEFALSEFALSEFALSE
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Source_Tissueskeletal/tissue/source elements, specific bone name should be reported with an underscore (e.g. bone_phalanx), multiple values separated by ;StringTRUEFALSEFALSEFALSEFALSE
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Nr_Librariesnumber of librariesIntegerFALSEFALSEFALSEFALSEFALSE
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Library_Namesidentifiers of the libraries used to generate the genotype data, multiple values separated by ;StringTRUEFALSEFALSEFALSEFALSE
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Capture_Typespecifics of data generation method, multiple values separated by ;StringTRUETRUEFALSEShotgun;1240K;ArborComplete;ArborPrimePlus;ArborAncestralPlus;TwistAncientDNA;OtherCapture;ReferenceGenomeFALSEFALSE
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UDG “mixed” in case multiple libraries with different UDG treatment were mergedStringFALSETRUEFALSEminus;half;plus;mixedFALSEFALSE
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Library_Built“ds” for double stranded, “ss” for single stranded, “mixed” in case multiple libraries with different protocols were mergedStringFALSETRUEFALSEds;ss;otherFALSEFALSE
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UDG UDG treatment, “mixed” in case multiple libraries with different UDG treatment were mergedStringFALSETRUEFALSEminus;half;plus;mixedFALSEFALSE
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Library_Builtstrandedness, “mixed” in case multiple libraries with different protocols were mergedStringFALSETRUEFALSEds;ss;mixedFALSEFALSE
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Genotype_Ploidyploidy of the genotypesStringFALSETRUEFALSEdiploid;haploidFALSEFALSE
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Data_Preparation_Pipeline_URLURL pointing to a description of the pipeline used to generate the genotype data from the source dataStringFALSEFALSEFALSEFALSEFALSE
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Endogenous% endogenous DNA as estimated from SG libraries (before capture), as for example estimated by EAGER, not on target and no quality filter, in case of multiple libraries report only the highest valueFloatFALSEFALSETRUE0100FALSEFALSE
sample_accessionThe sample accession code as used in INSDC databases, including ENA and SRA (Example: SAMEA7050454)StringFALSEFALSEFALSETRUETRUE
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study_accessionThe study accession code as used in INSDC databases, including ENA and SRA (Example: PRJEB39316)StringFALSEFALSEFALSEFALSEFALSE
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run_accessionThe run accession code as used in INSDC databases, including ENA and SRA (Example: ERR4331996)StringFALSEFALSEFALSEFALSEFALSE
@@ -19,4 +20,4 @@ fastq_aspera The Aspera-link (URL) to the FASTQ-file(s). (Example: fasp.sra.ebi.
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fastq_bytesThe number of bytes of the FASTQ-file(s) in bytesIntegerTRUEFALSETRUE0InfFALSEFALSE
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fastq_md5The MD5 hash(es) of the FASTQ-file(s)StringTRUEFALSEFALSEFALSEFALSE
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read_countThe number of readsIntegerFALSEFALSETRUE0InfFALSEFALSE
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submitted_ftpThe URL(s) to the originally submitted file(s) before it got converted to FASTQ. This can sometimes be helpful for processingStringTRUEFALSEFALSEFALSEFALSE
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submitted_ftpThe URL(s) to the originally submitted file(s) before it got converted to FASTQ. This can sometimes be helpful for processingStringTRUEFALSEFALSEFALSEFALSE
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