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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 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



  1. A CyVerse account. (Register for an CyVerse account here -
  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"


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