Commit 35c4b240 authored by bow's avatar bow
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Update SAGE documentation

parent 6601f23d
# Introduction
# Sage
## Introduction
The Sage pipeline has been created to process SAGE data, which requires a different approach than standard NGS data.
### Modules and Tools
# Tools for this pipeline
This pipeline uses the following modules and tools:
* [Flexiprep](flexiprep.md)
* [Mapping](mapping.md)
......@@ -11,12 +15,17 @@ The Sage pipeline has been created to process SAGE data, which requires a differ
* [SageCreateTagCounts](../tools/sagetools.md)
# Example
## Configuration
Note that one should first create the appropriate [configs](../general/config.md).
To get the help menu:
## 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 Biopet-0.2.0.jar pipeline Sage -h
$ java -jar /path/to/biopet.jar pipeline sage -h
Arguments for Sage:
-outDir,--output_directory <output_directory> Output directory
--countbed <countbed> countBed
......@@ -27,15 +36,24 @@ Arguments for Sage:
-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:
~~~
java -jar Biopet-0.2.0-DEV-801b72ed.jar pipeline Sage -run --config MySamples.json --config --MySettings.json
biopet pipeline sage -config /path/to/config.json -qsub -jobParaEnv BWA -run
~~~
# Examine results
## 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`).
## Result files
~~~
.
├── 1A
......@@ -95,9 +113,3 @@ To run the pipeline:
   ├── no_sense_genes.txt
   └── tag.lib
~~~
## Best practice
# References
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