Quick start with the Tutorial Data Set
Before running your analyses you can use the the Tutorial Data Set to make and check your installation. First copy the configuration file corresponding to the test.
Then start the workflow.This will run the quality control of the raw FASTQ. See FASTQ quality control for detailed explanations. If everything goes find you will see the results in TestDataset/results/Test1/fastqc. See also how to follow your jobs to know how to check that the run went fine.
You can now move on with your own data, or run the rest of the workflow on the test dataset. To do so you have to modify configs/config_main.yaml turning QC entry from "yes" to "no". If you don't know how to do that, see Preparing the run. Then restart the workflow.
Detailed explanation of the outputs are available in Results.
Info
The Tutorial Data Set is taken from the publication:
Genome-wide analysis in the mouse embryo reveals the importance of DNA methylation for transcription integrity.
This study investigates (by WGBS) the impact of DNA methyltransferases depletion on the mouse methylome. The three biological conditions are :
- WT (Wild Type)
- 1KO (simple Knock-Out of DNMT1)
- DKO (double Knock-Out of DNMT3A/B)
The dataset was reduced to a portion of chromsome 19.
Scheme of DNMT1 and DNMT3A/B biological functions
