Some flanking markers require additional validation & post-processing - Githubissues

candYgene / pbg-ld

Linked Data Platform for Plant Breeding & Genomics

https://research-software.nl/software/pbg-ld

Apache License 2.0

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Some flanking markers require additional validation & post-processing #34

Closed arnikz closed 5 years ago

arnikz commented 5 years ago

For example, QTL:3464107_4_15 is associated with two (flanking) markers:

TG194-J1 tagged as
- TG194
  - http://localhost:8890/genome/Solanum_lycopersicum/variation/gene72_0-i22; chromosome 11:2947789-2948311
  - http://localhost:8890/genome/Solanum_lycopersicum/variation/gene73_0-i22; chromosome 11:2947789-2948309
- J1
  - http://localhost:8890/genome/Solanum_pennellii/variation/cLES-5-J1; chromosome 1:95577802-95577596 (which is orthologous to http://localhost:8890/genome/Solanum_lycopersicum/variation/gene358_0-i2; chromosome 1:85319942-85322549)

gurnoor1990 commented 5 years ago

Solved in the new data! which will be updated while solving issue #21

3464107 4 15 TG194-J1 http://solgenomics.net/genome/Solanum_lycopersicum/variation/gene358_0-i2; http://solgenomics.net/genome/Solanum_lycopersicum/variation/gene72_0-i22; http://solgenomics.net/genome/Solanum_lycopersicum/variation/gene73_0-i22; http://solgenomics.net/genome/Solanum_pennellii/variation/cLES-5-J1

arnikz commented 5 years ago

Requires revision of this code: https://github.com/candYgene/pbg-ld/blob/673ed9eb071a4ec7d1dbdaf323e690a81ab70669/src/update_rdf.sql#L497-L589

arnikz commented 5 years ago

The code is correct, however, the marker J1 (as indicated in the article) could be different from cLES-5-J1.