...
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 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
Pre-Requisites
- A CyVerse account. (Register for an CyVerse account here - user.cyverse.org)
- Input file(s)
- Input file Name: SAM files generated from any mapper
- Output
- Output File name: Name of the output file (output.sorted.bam is default)
- Cufflinks-2.2.1: Regarding parameters for this section, please refer to Cufflinks-2.2.1
- 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
- Input file: BowtieOutput.sam
- Output: Default file name
- 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"
| 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 |