{% extends "base.html" %} {% block content %}
Sample: {{ project }}
Type: {{ type }}
Pipeline: {{ pipeline_name }}
The following table gives some basic statistics about the raw data before any filtering. The A, C, G, T, N rows report the percentage of each bases in the overall sequences. The GC content is provided in percentage as well.
The following figure(s) gives the average quality (red line) of raw reads (500,000 at max). The x-axis being the length of the reads. The yellow enveloppe gives the variation of the quality (1 standard deviation).
Click on the image to jump to a full FastQC report.
We mapped the raw reads on a reference (see config file). The reads mapped are removed and the unmapped reads are kept. Here below are some statistics about the mapped and unmapped reads.
The A, C, G, T, N rows report the percentage of each bases in the overall sequences
{{ phix_stats }}Reads statistics after trimming and adapter removal. Again, the A, C, G, T, N rows report the percentage of each bases in the overall sequences
{{ cutadapt_stats1 }} The final FastQ files without adapters have the following characteristics: {{ cutadapt_stats2 }}The following figure(s) gives the average quality (red line) of raw reads (500,000 at max). The x-axis being the length of the reads. The yellow enveloppe gives the variation of the quality (1 standard deviation).
Click on the image to jump to a full FastQC report.
Overview of the Taxonomic content of the filtered reads.
The taxonomic analysis is performed with Kraken and the database {{ kraken_database }}. The analysis is performed with a Kmer approach. The details about the database itself are available in the Sequana documentation. The taxonomic analysis should give a good idea of the content of the FastQ files. It should be used as a sanity check. However, be aware that this is not a systematic analysis: some species may be absent and therefore will not appear. Besides, be aware that the more closely related two species are, the less precise will be the classification.
The following clickable image is a simplified version (only genus are shown) of an interactive and more detailled version. The unclassified part includes adapters or species not included in the database (eukaryotes except human)