@@ -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:
