uofs-pulse-binfo/tripal_qtl

Provides additional fields and data import which provide support for quantitative trait loci. Additionally, it integrates with Tripal Map through shared vocabulary terms and data storage models.

Tripal QTL (Tripal 3)

This module provides additional fields and data import which provide support for quantitative trait loci. Additionally, it integrates with Tripal Map through shared vocabulary terms and data storage models.

Installation

1. Install this module as you would any other Drupal module.
2. (Recommended) Install Tripal Map: https://gitlab.com/mainlabwsu/tripal_map

Usage

1. Load your genetic map using the MST Map Importer and then load the associated QTL using the QTL importer.
2. Go to Admin > Tripal > Data Storage > Chado > Materialized Views and populate tripal_map_genetic_markers_mview and tripal_map_qtl_and_mtl_mview. This will make your data available to Tripal Map and the fields provided to this module.
3. Go to the Tripal Map Quickstart at http://localhost/MapViewer and check your map out!
4. Create genetic map pages by going to Admin > Content > Tripal Content, click "Publish" and choose "Genetic Map" from the drop-down.

Importers

• Genetic Maps (MSTmap Format)
• Genetic Markers & Loci: COMING SOON
• Quantitative Trait Loci (QTL)

Documentation

We have extensive documentation for all our available importers including form screenshots, validation and data storage ER diagrams on ReadtheDocs.

tripal_qtl's Issues

Images in ReadtheDocs are indistinct

The images are actually in good quality but not displayed properly.
possible solution:
1, reload images, being too wide is likely the cause of image being indistinct
2, give a NOTE of viewing full image in new site

MSTMap Importer: Assumptions

1. All included markers are created as type genetic_marker with MAIN:marker_type as SNP.
2. Marker name and locus name are the same.

Feature Requests: MST Map loader

Allow link to original population through stock_featuremap.
Indicate publication/contacts during loading.

QTL Lists for various Tripal Content Pages

Content Types

• Genetic Maps
  • List QTL on the current map.
• Trait Pages
  • List QTL associated with the current trait through feature_cvterm.
• Genetic Marker Pages
  • List the QTL for markers within the confidence interval.

Columns

• genetic map w/ link,
• trait w/ link,
• QTL name w/ link,
• linkage group & position
• confidence interval
• peak lod
• additive effect w/ parent

Links

• If Tripal Map is installed then link to the MapViewer.
• If Tripal JBrowse is installed, link to JBrowse. For JBrowse we want tracks which highlight the markers within a QTL confidence interval (1 LOD drop). Ideally we would colour code these markers using a gradient with the darker colour nearest the peak.