Samtools_mapping_stats-1.0

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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