UHTS_Test_Plan

Owned by vaughne
Last updated: Jun 27, 2010Version comment
2 min read

List of Test Sets

  1. Preprocessing Data Sets
    1. Barcoded, pair-end sequence library
    2. Barcoded, single-end sequence library
    3. Sequence library with 3' adapter
  2. Variant Detection 1: Comparative sequencing of Arabidopsis thaliana ec. Landsberg
    1. UHTS_Test_VarDetect_1
  3. Variant Detection 2: SRA SRX010829: Genotyping Maize NAM parental line Mo17
    1. UHTS_Test_VarDetect_2
  4. Transcript Quantification 1: RNAseq Library; SRA accession SRX018907; Maize B73 leaf developmental gradient
    1. UHTS_Test_RNAseq_1
  5. Transcript Quantification 2: Strand-specific RNAseq; Arabidopsis thaliana library RMMT
    1. UHTS_Test_RNAseq_2

Assignments

Tester

Test Case

Notes

Chunlao Tang

UHTS_Test_Barcode_PE,UHTS_Test_Barcode_SE,UHTS_Test_VarDetect_1

 

Liya Wang

UHTS_Test_3prime,UHTS_Test_RNAseq_2

 

Matt Vaughn

UHTS_Test_RNAseq_1,UHTS_Test_VarDetect_2,UHTS_Test_Barcode_PE

 

Karla Gendler

UHTS_Test_VarDetect_1,UHTS_Test_RNAseq_1,UHTS_Test_Barcode_SE

 

Major functionalities

This release is designed to measure transcript abundance and facilitate detection of novel SNPs in maize and Arabidopsis. In addition, routine pre-processing such as barcode splitting, adapter trimming, quality score conversion, and quality filtering are supported. Data can be input via file upload from the user's desktop or via import of an FTP, HTTP URL. Also in this release is a file inspector function that allows users to preview very large files, such as those that might be used in or generated by UHTS activities.

How to report issues

iPlant uses JIRA to track and manage issues relating to the Discovery Environemnt. Issues connected to the DE are readable by anyone, but an iPlant account is required to create or modify an issue. Login to JIRA using your iPlant credentials. In the upper right hand corner, you will find links to create issues. Click this link (Create Issue).

Select the type of issue that you are reporting.

Fill in all the appropriate fields and click submit. For "Components", select "Ultra High Throughput Sequencing". In the environment section, fill in as much information about the browser that you are using (e.g. Firefox version 3.6). You will receive an email detailing your issue and will receive follow up emails as work progresses on the bug.

Documentation

  1. Matt will outline what needs to go in to the documentation (high-level science)
    1. NOTE: Under way with NH now
  2. Chunlao will fill in the details once UI details are firmed up