Commit 731d6089 authored by sajvanderzeeuw's avatar sajvanderzeeuw

added start up sage docs

parent 1a209ea0
......@@ -4,7 +4,7 @@
The GATK-pipeline is build for variant calling on NGS data (preferably Illumina data).
It is based on the <a href="https://www.broadinstitute.org/gatk/guide/best-practices" target="_blank">best practices</a>) of GATK in terms of there approach to variant calling.
The pipeline accepts ```.fastq & .bam``` files as <samplename>.
The pipeline accepts ```.fastq & .bam``` files as input.
----
......
# Introduction
The Sage pipeline has been created to process SAGE data, which requires a different approach than NGS data.
The Sage pipeline has been created to process SAGE data, which requires a different approach than standard NGS data.
# Tools for this pipeline
* [Flexiprep](flexiprep.md)
* [Mapping](mapping.md)
* [SageCountFastq](sagetools.md)
* [SageCreateLibrary](sagetools.md)
* [SageCreateTagCounts](sagetools.md)
# Invocation
# Example
Note that one should first create the appropriate [configs](../config.md).
~~~
java -jar Biopet-0.2.0-DEV-801b72ed.jar pipeline Sage -h
java -jar Biopet-0.2.0.jar pipeline Sage -h
Arguments for Sage:
-outDir,--output_directory <output_directory> Output directory
--countbed <countbed> countBed
......@@ -20,13 +26,70 @@ Arguments for Sage:
~~~
# Testcase A
# Testcase B
# Examine results
## Result files
~~~
.
├── 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
~~~
## Best practice
......
......@@ -11,13 +11,13 @@ so usually one does not want to safe these files.
## Example
To start the tool:
~~~
java -jar Biopet-0.2.0-DEV-801b72ed.jar tool mpileupToVcf
java -jar Biopet-0.2.0.jar tool mpileupToVcf
~~~
To open the help:
~~~bash
java -jar Biopet-0.2.0-DEV-801b72ed.jar tool mpileupToVcf -h
java -jar Biopet-0.2.0.jar tool mpileupToVcf -h
Usage: MpileupToVcf [options]
-l <value> | --log_level <value>
......
# SAGE tools
## SageCountFastq
~~~
Usage: SageCountFastq [options]
-l <value> | --log_level <value>
Log level
-h | --help
Print usage
-v | --version
Print version
-I <file> | --input <file>
-o <file> | --output <file>
~~~
## SageCreateLibrary
~~~
Usage: SageCreateLibrary [options]
-l <value> | --log_level <value>
Log level
-h | --help
Print usage
-v | --version
Print version
-I <file> | --input <file>
-o <file> | --output <file>
--tag <value>
--length <value>
--noTagsOutput <file>
--noAntiTagsOutput <file>
--allGenesOutput <file>
~~~
## SageCreateTagCounts
~~~
Usage: SageCreateTagCounts [options]
-l <value> | --log_level <value>
Log level
-h | --help
Print usage
-v | --version
Print version
-I <file> | --input <file>
-t <file> | --tagLib <file>
--countSense <file>
--countAllSense <file>
--countAntiSense <file>
--countAllAntiSense <file>
~~~
\ No newline at end of file
......@@ -9,6 +9,8 @@ pages:
- ['pipelines/sage.md', 'Pipelines', 'Sage']
- ['tools/SamplesTsvToJson.md','tools','SamplesTsvToJson']
- ['tools/BastyGenerateFasta.md','tools','BastyGenerateFasta']
- ['tools/MpileupToVcf.md', 'tools', 'MpileupToVcf']
- ['tools/sagetools.md', 'tools', 'Sagetools']
- ['cluster/oge.md', 'OpenGridEngine']
- ['about.md', 'About']
- ['license.md', 'License']
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment