@@ -94,6 +94,195 @@ If singularity was selected in installation of RNAja, it could be needed to give
**Important Note** : In IRD "i-Trop" cluster, run RNAja using ONLY a node, data has to be in "/scratch" of chosen node. Use `nodelist : nodeX` parameter inside of `cluster_config.yaml`̀ file.
## 3. Running your data
### 3.1.create a pipeline by configuring the `config.yaml` file
Before to run RNAja, create a `config.yaml` by using before to adapt it.
```
RNAja create_config
```
Three sections are needed for RNAja into the `config.yaml` file: section DATA, MODE and PARAMS.
### DATA section
Adapt `config.yaml` file with path to fastq files, reference and annotation file in the `DATA section` as well as the output directory.
Into the `sample_info` DATA key, you need to give a comma separated `sample_info.txt` file containing information about samples. This file needs header with Forward,Reverse,SampleName,Direction,Treatment,Experiment columns.
If you are in single mode, don't fill on 'reverse' column in `sample_info.txt` file
Finally, you need confirm if reads are paired or single filling in `PAIRED` param using `true` or `false` boolean. If PAIRED : true, samples suffix should be `_R1.fastq.gz` and `_R2.fastq.gz`.
ATTENTION : If yours reads are ilumina paired, you need rename reads SAMPLE_R1.fastq.gz and SAMPLE_R2.fastq.gz. For single reads use SAMPLE_R1.fastq.gz. RNAja uses compressed and decompressed fastq files.
#### de_comparisons key
In the `de_comparisons` indicate the path to the treatementsComparaison file. This file is used to differential expression analysis. Please declare treatments you want to compare. Here an example. RNAja expects a header with condA and CondB comma separated columns :
```commandline
condA,condB
Batch,CENPK
```
### MODE section
Five pipelines can be running in parallel by using RNAja !
We have included for instance two mappers (STAR and HISAT2) and 3 counters (STRINGTIE, HTSEQCOUNT,STAR). You can activate or deactivate pipelines you would run in the MODE section such as ...
```
MODE:
HISAT2_STRINGTIE: true
HISAT2_HTSEQCOUNT: true
STARmap_STARcount: true
STARmap_HTSEQCOUNT: true
STARmap_STRINGTIE: true
```
### PARAMS section
In the PARAMS section, tools parameters can be modified and adapted.
You can modify `HISAT2` indexation, `STAR` indexation and mapping options, change `STRINGTIE` mode (discovery or not) as well as `HTSEQCOUNT` params. Feel free to check documentation of these tools before to run RNAja!
#### output
Here an example of `output_dir` if you have activated all five pipelines proposed by RNAja.
