Samtools_mapping_stats-1.0
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The DE Quick Start tutorial provides an introduction to basic DE functionality and navigation.
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
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Pre-Requisites
- A CyVerse account. (Register for an CyVerse account here -Â user.cyverse.org)
- Input file(s)
- Input folder name: A folder consisting of sorted bam files
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The test data for testing QUAST in here :Â /iplant/home/shared/iplantcollaborative/example_data/samtools_mapping_stats
Test run
- Input file:Â samtools_mapping_stats
Test Results
Successful execution of the Samtools_mapping_stats-1.0 will create a output file - "bam_stats.txt"
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Sample_name | Mapped_reads | Unmapped_reads | Total_reads |
samtools_mapping_stats/sample_1.bam | 11762 | 0 | 11762 |
samtools_mapping_stats/sample_2.bam | 11762 | 0 | 11762 |
samtools_mapping_stats/sample_3.bam | 11762 | 0 | 11762 |
samtools_mapping_stats/sample_4.bam | 11762 | 0 | 11762 |
samtools_mapping_stats/sample_5.bam | 11762 | 0 | 11762 |
samtools_mapping_stats/sample_6.bam | 11762 | 0 | 11762 |
samtools_mapping_stats/sample_7.bam | 11755 | 7 | 11762 |