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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 can be used to run Cufflinks-2.2.1 using SAM files instead of BAM files. This app is basically a workflow that consists of two apps


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 file Name: SAM files generated from any mapper
  3. Output
    1. Output File name: Name of the output file (output.sorted.bam is default)
  4. Cufflinks-2.2.1: Regarding parameters for this section, please refer to Cufflinks-2.2.1
    1. 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-SAMtoSortedBAMsamtools_mapping_stats

Test run

  1. Input file: BowtieOutput.sam
  2. Output: Default file name
  3. Cufflinks-2.2.1: Leave everything default samtools_mapping_stats

Test Results


Successful execution of the QUAST assessment pipeline will create the following files and folders:


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