Commit 06f6747b authored by Moustakas's avatar Moustakas
Browse files

Fix picard tool usage Code. Replace JSON with YAML examples

parent 6236765b
......@@ -32,48 +32,34 @@ To get help creating the appropriate [configs](../general/config.md) please refe
Samples are single experimental units whose expression you want to measure. They usually consist of a single sequencing library, but in some cases (for example when the experiment demands each sample have a minimum library depth) a single sample may contain multiple sequencing libraries as well. All this is can be configured using the correct JSON nesting, with the following pattern:
~~~ json
{
"samples": {
"sample_A": {
"libraries": {
"lib_01": {
"R1": "/absolute/path/to/first/read/pair.fq",
"R2": "/absolute/path/to/second/read/pair.fq"
}
}
}
}
}
~~~ yaml
---
samples:
sample_A:
libraries:
lib_01:
R1: "/absolute/path/to/first/read/pair.fq"
R2: "/absolute/path/to/second/read/pair.fq"
~~~
In the example above, there is one sample (named `sample_A`) which contains one sequencing library (named `lib_01`). The library itself is paired end, with both `R1` and `R2` pointing to the location of the files in the file system. A more complicated example is the following:
~~~ json
{
"samples": {
"sample_X": {
"libraries": {
"lib_one": {
"R1": "/absolute/path/to/first/read/pair.fq",
"R2": "/absolute/path/to/second/read/pair.fq"
}
}
},
"sample_Y": {
"libraries": {
"lib_one": {
"R1": "/absolute/path/to/first/read/pair.fq",
"R2": "/absolute/path/to/second/read/pair.fq"
},
"lib_two": {
"R1": "/absolute/path/to/first/read/pair.fq",
"R2": "/absolute/path/to/second/read/pair.fq"
}
}
}
}
}
~~~ yaml
---
samples:
sample_X:
libraries:
lib_one:
R1: "/absolute/path/to/first/read/pair.fq"
R2: "/absolute/path/to/second/read/pair.fq"
sample_Y:
libraries:
lib_one:
R1: "/absolute/path/to/first/read/pair.fq"
R2: "/absolute/path/to/second/read/pair.fq"
lib_two:
R1: "/absolute/path/to/first/read/pair.fq"
R2: "/absolute/path/to/second/read/pair.fq"
~~~
In this case, we have two samples (`sample_X` and `sample_Y`) and `sample_Y` has two different libraries (`lib_one` and `lib_two`). Notice that the names of the samples and libraries may change, but several keys such as `samples`, `libraries`, `R1`, and `R2` remain the same.
......@@ -85,7 +71,7 @@ For the pipeline settings, there are some values that you need to specify while
1. `output_dir`: path to output directory (if it does not exist, Gentrap will create it for you).
2. `aligner`: which aligner to use (`gsnap`, `tophat`, `hisat2`, `star` or `star-2pass`). `star-2pass` enables the 2-pass mapping option of STAR, for the most sensitive novel junction discovery. For more, please refer to [STAR user Manual](https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf)
3. `reference_fasta`: this must point to a reference FASTA file and in the same directory, there must be a `.dict` file of the FASTA file. If the `.dict` file does not exist, you can create it using: ```` java -jar CreateSequenceDictionary.jar R= yourReference.fasta O= yourReference.dict ````
3. `reference_fasta`: this must point to a reference FASTA file and in the same directory, there must be a `.dict` file of the FASTA file. If the `.dict` file does not exist, you can create it using: ```` java -jar <picard jar> CreateSequenceDictionary R=<reference.fasta> O=<outputDict> ````
4. `expression_measures`: this entry determines which expression measurement modes Gentrap will do. You can choose zero or more from the following: `fragments_per_gene`, `base_counts`, `cufflinks_strict`, `cufflinks_guided` and/or `cufflinks_blind`. If you only wish to align, you can set the value as an empty list (`[]`).
5. `strand_protocol`: this determines whether your library is prepared with a specific stranded protocol or not. There are two protocols currently supported now: `dutp` for dUTP-based protocols and `non_specific` for non-strand-specific protocols.
6. `annotation_refflat`: contains the path to an annotation refFlat file of the entire genome
......@@ -99,28 +85,29 @@ While optional settings are:
5. `call_variants`: whether to call variants on the RNA-seq data or not, defaults to `false`.
Thus, an example settings configuration is as follows:
~~~ json
{
"output_dir": "/path/to/output/dir",
"expression_measures": ["fragments_per_gene", "bases_per_gene"],
"strand_protocol": "dutp",
"reference_fasta": "/path/to/reference/fastafile",
"annotation_gtf": "/path/to/gtf",
"annotation_refflat": "/path/to/refflat"
}
~~~ yaml
---
output_dir: "/path/to/output/dir"
expression_measures:
- "fragments_per_gene"
- "bases_per_gene"
strand_protocol: "dutp"
reference_fasta: "/path/to/reference/fastafile"
annotation_gtf: "/path/to/gtf"
annotation_refflat: "/path/to/refflat"
~~~
#### Best practice example
If you are unsure of how to use the numerous options of gentrap, please refer to the following best practice configuration file example.
~~~ json
{
"output_dir": "/path/to/output/dir",
"aligner": "gsnap",
"reference_fasta": "/path/to/reference/fastafile",
"expression_measures": ["fragments_per_gene"],
"strand_protocol": "dutp",
"annotation_refflat": "/path/to/refflat"
}
~~~ yaml
---
output_dir: "/path/to/output/dir"
aligner: "gsnap"
reference_fasta: "/path/to/reference/fastafile"
expression_measures:
- "fragments_per_gene"
strand_protocol: "dutp"
annotation_refflat: "/path/to/refflat"
~~~
#### Example configurations
......@@ -138,7 +125,7 @@ biopet pipeline gentrap -config </path/to/config.json> -qsub -jobParaEnv BWA -ru
You can also use the `biopet` environment module (recommended) when you are running the pipeline in SHARK:
~~~ bash
$ module load biopet/v0.5.0
$ module load biopet/v0.7.0
$ biopet pipeline gentrap -config </path/to/config.json> -qsub -jobParaEnv BWA -run
~~~
......
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