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SAM_to_Sorted_BAM-0.1.9

SAM_to_Sorted_BAM-0.1.9

Jun 16, 2017

 

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 can be used to convert SAM file to Sorted BAM file which is generally needed for downstream bioinformatics tools.

 

Pre-Requisites

  1. A CyVerse account. (Register for an CyVerse account here - user.cyverse.org)

  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)

     

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 (BowtieOutput.sorted)

  3.  

Test Results

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

  1. logs

  2. BowtieOutput.sorted

  3. BowtieOutput.sorted.bam.bai