Cufflinks_from_SAM-2.2.1 in DE



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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.

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



  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


Test/sample data

The test data for testing QUAST in here : /iplant/home/shared/iplantcollaborative/example_data/Samtools-SAMtoSortedBAM

Test run

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

Test Results

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

  1. logs
  2. output_out: This folder contains cufflinks related outputs (genes.fpkm_tracking, isoforms.fpkm_tracking, skipped.gtf and transcripts.gtf)
  3. output.sorted.bam
  4. output.sorted.bam.bam.bai