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Parasitoid Wasps Project: Annotation Workbook

  • November 22, 2021December 1, 2021

For the Parasitoid Wasps Project gene annotation, project submission will consist of a completed Annotation Workbook, a screenshot of the user track on the Genome Browser, and sequence files for the entire transcript and encoded protein. This Annotation Workbook is an Excel file with space to fill out all the necessary information for the gene annotation.

If it is done correctly, filling out the workbook will also auto-populate a GFF file that can be used for testing the accuracy of gene models (described in the “Checking Accuracy of the Gene Model (Alternative to Gene Model Checker)” section of the “Annotation Workbook Directions“). Please note that everything should be filled out exactly as described: the vocabulary and formatting need to be very precise to make a functional GFF file.

The “Example” sheet has been completed for you to reference while completing the “Transcript” sheet.

Parasitoid Wasps Project: Annotation Workbook Directions

  • November 22, 2021December 1, 2021

This document provides directions for how to complete and obtain the items needed to submit a Parasitoid Wasps Project annotation—a completed Annotation Workbook, a screenshot of the user track on the Genome Browser, and sequence files for the entire transcript and encoded protein.

Pathways Project: Annotation Report

  • September 14, 2020March 11, 2022

GEP students will use the Report Form document to submit their annotation results for the Pathways Project. The Project Details Table handout will show students how to fill out the first page of the Annotation Report. The Report Form Exemplar is provided as an example of a completed report.

Pathways Project: Annotation Notebook

  • September 14, 2020August 31, 2021

The Pathways Annotation Notebook will help GEP students keep track of their work as they are annotating, and then they can use the notebook to fill out the report form. This notebook does not have to be submitted to GEP, it’s just an extra resource students might find helpful.

Common Finishing Errors

  • August 15, 2020August 19, 2020

This PowerPoint presentation describes the common errors observed in student finishing projects.

Finishing Checklist

  • August 15, 2020August 19, 2020

Students should complete all items on this checklist before submitting the project back to the GEP.

Strategies for Finishing Hybrid Assemblies

  • August 15, 2020August 19, 2020

This document contains advice on the strategies students can use to resolve common problems they may encounter during sequence improvement.

Calling Additional Reads

  • August 15, 2020August 19, 2020

Students will typically need to request additional sequencing reactions in order to improve the quality of an assembly. This document describes some of the key considerations that students should keep in mind when they design oligonucleotide primers.