The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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The CyVerse App Store is currently being restructured, and apps are being moved to an HPC environment. During this transition, users may occasionally be unable to locate or use apps that are listed in our tutorials. In many cases, these apps can be located by searching them using the search bar at the top of the Apps window in the DE. To increase the chance for search success, try not searching the entire app name and version number but only the portion that refers to the app's function or origin (e.g. 'SOAPdenovo' instead of 'SOAPdenovo-Trans 1.01').

Also, as part of the 2.8 app categorization, a number of apps were deprecated and are no longer available, and there is no longer an Archive category. You can search for a suitable replacement in the List of Applications in this window, or search on an app name or tool used for an app in the Apps window search field. If you need an app reinstated, please contact support@cyverse.org.


The DE Quick Start tutorial provides an introduction to basic DE functionality and navigation.

Please work through the tutorial and add your comments on the bottom of this page. Or send comments per email to support@cyverse.org. Thank you.

Rationale and background:

This app accepts a folder as an input and generates a table that consists of mapped, unmapped and total mapped reads using samtools command

 

Pre-Requisites

  1. A CyVerse account. (Register for an CyVerse account here - user.cyverse.org)
  2. Input file(s)
    1. Input folder name: A folder consisting of sorted bam files

     

Test/sample data

The test data for testing QUAST in here : /iplant/home/shared/iplantcollaborative/example_data/samtools_mapping_stats

Test run

  1. Input file: samtools_mapping_stats

Test Results

Successful execution of the Samtools_mapping_stats-1.0 will create a output file - "bam_stats.txt"

 

Sample_nameMapped_readsUnmapped_readsTotal_reads
samtools_mapping_stats/sample_1.bam 11762011762
samtools_mapping_stats/sample_2.bam 11762011762
samtools_mapping_stats/sample_3.bam 11762011762
samtools_mapping_stats/sample_4.bam 11762011762
samtools_mapping_stats/sample_5.bam 11762011762
samtools_mapping_stats/sample_6.bam 11762011762
samtools_mapping_stats/sample_7.bam 11755711762



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