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:

• Flexiprep
• Mapping
• SageCountFastq
• SageCreateLibrary
• SageCreateTagCounts

Configuration and flags

Note that one should first create the appropriate configs.

Please see the documentation for wrapped pipelines (Mapping and Flexiprep) for their configuration options and flags.

Specific configuration values for the Sage pipeline are:

Name	Type	Function
countbed	Path (required)	Path to count bed file
squishedcountbed	Path (optional)	By supplying this file the auto squish job will be skipped
transcriptome	Path (required)	Fasta file for transcriptome. Note: Must come from Ensembl!
tags_library	Path (optional)	Five-column tab-delimited file ( ). Unsupported option

Sample input extensions

Please refer to our mapping pipeline for information about how the input samples should be handled.

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:

$ biopet pipeline sage -h

Arguments for Sage:
 -s,--sample <sample>                  Only Sample
 -config,--config_file <config_file>   JSON / YAML config file(s)
 -cv,--config_value <config_value>     Config values, value should be formatted like 'key=value' or
                                       'path:path:key=value'
 -DSC,--disablescatter                 Disable all scatters

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

$ module load biopet/v0.5.0
$ 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

Getting Help

If you have any questions on running SAGE or suggestions on how to improve the overall flow, feel free to post an issue to our issue tracker at GitHub. Or contact us directly via: SASC email