Sage

Introduction

The Sage pipeline has been created to process SAGE data, which requires a different approach than standard NGS data.

Modules and Tools

This pipeline uses the following modules and tools:

Configuration

Note that one should first create the appropriate configs.

Running Sage

As with other pipelines, you can run the Sage pipeline by invoking the pipeline subcommand. There is also a general help available which can be invoked using the -h flag:

$ java -jar /path/to/biopet.jar pipeline sage -h

Arguments for Sage:
 -outDir,--output_directory <output_directory>   Output directory
 --countbed <countbed>                           countBed
 --squishedcountbed <squishedcountbed>           squishedCountBed, by suppling this file the auto squish job will be 
                                                 skipped
 --transcriptome <transcriptome>                 Transcriptome, used for generation of tag library
 -config,--config_file <config_file>             JSON config file(s)
 -DSC,--disablescatterdefault                    Disable all scatters

If you are on SHARK, you can also load the biopet module and execute biopet pipeline instead:

$ module load biopet/v0.3.0
$ biopet pipeline sage

To run the pipeline:

 biopet pipeline sage -config /path/to/config.json -qsub -jobParaEnv BWA -run

Output Files

Below is an example of the output files that you will get after running Sage. Here, we have two samples (1A and 1B) and each sample has two libraries (run_1 and run_2).

.
├── 1A
│   ├── 1A-2.merge.bai
│   ├── 1A-2.merge.bam
│   ├── 1A.fastq
│   ├── 1A.genome.antisense.counts
│   ├── 1A.genome.antisense.coverage
│   ├── 1A.genome.counts
│   ├── 1A.genome.coverage
│   ├── 1A.genome.sense.counts
│   ├── 1A.genome.sense.coverage
│   ├── 1A.raw.counts
│   ├── 1A.tagcount.all.antisense.counts
│   ├── 1A.tagcount.all.sense.counts
│   ├── 1A.tagcount.antisense.counts
│   ├── 1A.tagcount.sense.counts
│   ├── run_1
│   │   ├── 1A-1.bai
│   │   ├── 1A-1.bam
│   │   ├── flexiprep
│   │   └── metrics
│   └── run_2
│       ├── 1A-2.bai
│       ├── 1A-2.bam
│       ├── flexiprep
│       └── metrics
├── 1B
│   ├── 1B-2.merge.bai
│   ├── 1B-2.merge.bam
│   ├── 1B.fastq
│   ├── 1B.genome.antisense.counts
│   ├── 1B.genome.antisense.coverage
│   ├── 1B.genome.counts
│   ├── 1B.genome.coverage
│   ├── 1B.genome.sense.counts
│   ├── 1B.genome.sense.coverage
│   ├── 1B.raw.counts
│   ├── 1B.tagcount.all.antisense.counts
│   ├── 1B.tagcount.all.sense.counts
│   ├── 1B.tagcount.antisense.counts
│   ├── 1B.tagcount.sense.counts
│   ├── run_1
│   │   ├── 1B-1.bai
│   │   ├── 1B-1.bam
│   │   ├── flexiprep
│   │   └── metrics
│   └── run_2
│       ├── 1B-2.bai
│       ├── 1B-2.bam
│       ├── flexiprep
│       └── metrics
├── ensgene.squish.bed
├── summary-33.tsv
├── taglib
    ├── no_antisense_genes.txt
    ├── no_sense_genes.txt
    └── tag.lib