This space is home to learning materials and tutorials created for CyVerse products and services. To search the entire CyVerse wiki, use the box at the upper right.


LEARNING MATERIALS
 

 

 

 

 

 

Skip to end of metadata
Go to start of metadata

You are viewing an old version of this page. View the current version.

Compare with Current View Page History

« Previous Version 9 Next »

About this page

This page lists all current tutorials for all platforms.

  • Global search: To search on a word or phrase in any cell, click in the Global Filter field to the right and begin entering the query.
  • Sorting: To sort on a column, hover over the column header and click the arrow.
  • Filtering: To filter on a column, enter the first few letters of the item in the search field for that column.
  • To open the tutorial, click the link the App/Workflow Name column.
  • To email the tutorial's author, click the link on the author's name.
  • To view the user manual for an app used in the tutorial, click the link in the Apps Used column.

Table Filter Plugin license is not active, please generate a trial license or purchase the product.
App/Workflow NameAuthorCreatedUpdatedPlatformTypeAreaGoalApps UsedMajor Steps (do we need this?)
Evaluate and Pre-Process Sequencing ReadsBarthelson6/12/14

7/21/15

DEWorkflowRead cleanupClean and filter Illumina reads using DE apps.
  1. FastQC 0.10.1 (multi-file)
  2. Scythe-adapter-trimming
  3. Sickle-quality-based-trimming
  4. Prinseq-Graph-noPCA evaluate reads

Evaluate read quality, Remove adapter sequences, Filter sequences by quality, Reevaluate read-quality of the cleaned reads, Use an alternative method to evaluate read-quality

BLAST a TranscriptomeHilgert7/21/147/21/15DEWorkflow 

Become familiar with a procedure to reduce the number of transcripts and the level of redundancy in an assembled transcriptome, and to identify coding sequences that can be submitted to BLASTP searches.

  1. Select contigs
  2. CD-HIT-est 4.6.1
  3. Transcript decoder 1.0
  4. Blastp-2.2.29
    OR: DeltaBLAST-2.2.29

Eliminate small transcripts, Reduce transcript redundancy, Identify and translate coding sequences, Submit translated transcriptome to BLASTP OR: Submit translated transcriptome to Delta-BLAST

Assemble a Genome Using SOAPdenovo

Barthelson4/15/157/21/15DEWorkflow 

Gain familiarity with a commonly used procedure for de novo whole genome assembly of Illumina reads using the DE. Includes assembly of paired and unpaired Illumina reads with SOAPdenovo2, followed by an analysis of the assembly quality.

  1. SOAPdenovo 2.0.4
  2. Assess assembly vs whole genome

Assemble reads, Assess assembly

          
          
          
          
          
          
          
          
          
          
          
          
          
          
  • No labels