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mostly for issues pertaining to the content of the legumeinfo datastore; may also relate to characteristics of its user interface or managing the mirroring process to the legfed instance
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Missing peanut QTL data and markers #66

Closed svengato closed 1 year ago

svengato commented 2 years ago

In v2/Arachis/hypogaea/genetic, the only collection that yields QTL data (for ZZBrowse) was Tifrunner_x_GT-C20.gen.Agarwal_Clevenger_2018.

TG26_x_GPBD4.gen.Sarvamanga_Gowdaa_2011 - missing the .qtlmrk.tsv.gz file Tifrunner_x_GT-C20.gen.Wang_Penmetsa_2012 - missing the .qtlmrk.tsv.gz and .obo.tsv.gz files VG9514_x_TAG24.gen.Mondal_Hadapad_2014 - missing the .qtlmrk.tsv.gz and .obo.tsv.gz files

The rest have all required files, but their markers must not match any from v2/Arachis/hypogaea/markers : Huayu28_x_P76.gen.Hu_Zhang_2018 SunOleic97R_x_NC94022.gen.Qin_Feng_2012 TAG24_x_GPBD4.gen.Kolekar_Sujay_2016 Tifrunner_x_GT-C20.gen.Qin_Feng_2012

sammyjava commented 2 years ago

Assigning to Steven since he's our Trusty Genetics Guy. Reassign to me, Steven, if you'd like me to dig into this. I presume it's nontrivial to find the genomic mappings of the markers from those four collections. (Which is fine as far as mine loading goes, they don't have to have genomic positions.)

StevenCannon-USDA commented 2 years ago

Accepted - though I probably won't be able to get to it this week. Working through a backlog now.

sammyjava commented 2 years ago

UPDATE. All three of the GWAS have marker sets, but I've updated the names, which may affect you, @svengato :

NAMFlor7.gwas.Gangurde_Wang_2020/README.NAMFlor7.gwas.Gangurde_Wang_2020.yml:genotyping_platform: Axiom_Arachis_58K
NAMTifr.gwas.Gangurde_Wang_2020/README.NAMTifr.gwas.Gangurde_Wang_2020.yml:genotyping_platform: Axiom_Arachis_58K
USPeanutCore.gwas.Otyama_Kulkarni_2020/README.USPeanutCore.gwas.Otyama_Kulkarni_2020.yml:genotyping_platform: Axiom_Arachis2

corresponding to marker sets:

Tifrunner.gnm1.mrk.Axiom_Arachis_58K
Tifrunner.gnm1.mrk.Axiom_Arachis2

As for the QTL experiments, only one has an existing marker set:

Tifrunner_x_GT-C20.gen.Agarwal_Clevenger_2018/README.Tifrunner_x_GT-C20.gen.Agarwal_Clevenger_2018.yml:genotyping_platform: Agarwal_Clevenger_2018

corresponding to:

Tifrunner.gnm1.mrk.Agarwal_Clevenger_2018

So the markers in the other genetic collections remain to be found:

Huayu28_x_P76.gen.Hu_Zhang_2018/arahy.Huayu28_x_P76.gen.Hu_Zhang_2018.mrk.tsv.gz
ICGS44_x_ICGS76.gen.Gautami_Pandey_2012/arahy.ICGS44_x_ICGS76.gen.Gautami_Pandey_2012.mrk.tsv.gz
ICGS76_x_CSMG84.gen.Gautami_Pandey_2012/arahy.ICGS76_x_CSMG84.gen.Gautami_Pandey_2012.mrk.tsv.gz
mixed.gen.Gautami_Pandey_2012/arahy.mixed.gen.Gautami_Pandey_2012.mrk.tsv.gz
mixed.gen.Sujay_Gowda_2012/arahy.mixed.gen.Sujay_Gowda_2012.mrk.tsv.gz
TAG24_x_GPBD4.gen.Kolekar_Sujay_2016/arahy.TAG24_x_GPBD4.gen.Kolekar_Sujay_2016.mrk.tsv.gz
TAG24_x_ICGV86031.gen.Ravi_Vadez_2011/arahy.TAG24_x_ICGV86031.gen.Ravi_Vadez_2011.mrk.tsv.gz
TG26_x_GPBD4.gen.Sarvamanga_Gowdaa_2011/arahy.TG26_x_GPBD4.gen.Sarvamanga_Gowdaa_2011.mrk.tsv.gz
TG26_x_GPBD4.gen.Sujay_Gowda_2012/arahy.TG26_x_GPBD4.gen.Sujay_Gowda_2012.mrk.tsv.gz
Tifrunner_x_GT-C20.gen.Qin_Feng_2012/arahy.Tifrunner_x_GT-C20.gen.Qin_Feng_2012.mrk.tsv.gz
Tifrunner_x_GT-C20.gen.Wang_Penmetsa_2012/arahy.Tifrunner_x_GT-C20.gen.Wang_Penmetsa_2012.mrk.tsv.gz
VG9514_x_TAG24.gen.Mondal_Hadapad_2014/arahy.VG9514_x_TAG24.gen.Mondal_Hadapad_2014.mrk.tsv.gz
sammyjava commented 2 years ago

I'll work on all these before the next PeanutMine build. I'm on a new get-the-genetic-data-in-good-shape crusade.

sammyjava commented 1 year ago

I think this is all sorted as well, as ArachisMine loaded fine.