Before launching the pipeline

When you prepare the pipeline, a few information are printed on the screen. Check for:

1. the number of samples (should be >0)
2. check the content of the script fastqc.sh, especially on a SLURM cluster to check the slurm options.

After the pipeline has finished:

1. check that the file summary.html exists. If not, it means something went wrong in creating the HTML file. If so, check whether the file multiqc/multiqc_report.html exists
2. Open the file summary.html. This is were your expertise will now be required. To help you deciphering the fastqc and multiqc reports, you should look at the fastqc manual: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ to get help.

You may also find convenient to visit the drylab page of the biomics platform: https://biomics.pasteur.fr/drylab/ to get more help. In particular, please look at this PDF document: https://biomics.pasteur.fr/drylab/of_demutiplexing_and_fastqc.pdf