Check list

Before launching the pipeline

1. check the message on the screen. You should see the number of samples, check wether the pipeline see them as single-end data or paired data.
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