diff --git a/public/examples/bs-seq/multiqc_config.yaml b/public/examples/bs-seq/multiqc_config.yaml new file mode 100644 index 0000000..4548503 --- /dev/null +++ b/public/examples/bs-seq/multiqc_config.yaml @@ -0,0 +1,14 @@ +module_order: + - "bismark" + - "cutadapt" + - "fastqc": + name: "FastQC: trimmed" + anchor: "fqc_trimmed" + path_filters: + - "*_trimmed*" + - "fastqc": + name: "FastQC: raw" + anchor: "fqc_raw" + path_filters_exclude: + - "*_trimmed*" + generalstats: false diff --git a/public/examples/bs-seq/multiqc_report.html b/public/examples/bs-seq/multiqc_report.html index 54d87d6..32f67f8 100644 --- a/public/examples/bs-seq/multiqc_report.html +++ b/public/examples/bs-seq/multiqc_report.html @@ -23,7 +23,7 @@ MultiQC Report - + @@ -829,7 +829,7 @@ cursor: pointer; color: #ccc; } -.mqc_configModal_table tbody .sorthandle { +.mqc_config_modal_table tbody .sorthandle { color: #999; } .mqc_table .rowheader { @@ -1097,6 +1097,31 @@ font-family: "Lucida Grande", "Lucida Sans 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@@ -1249,6 +1274,7 @@ + +

Quality control tool for high throughput sequencing data.URL: http://www.bioinformatics.babraham.ac.uk/projects/fastqc

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Sequence Counts - @@ -6474,7 +6631,7 @@

Sequence counts for each sample. Duplicate read counts are an estimate only.

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This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

You can read more about duplicate calculation in the @@ -6491,16 +6648,19 @@

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Created with MultiQC
@@ -6515,12 +6675,12 @@

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Sequence Quality Histograms - @@ -6530,7 +6690,7 @@

The mean quality value across each base position in the read.

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To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

Taken from the FastQC help:

@@ -6545,14 +6705,17 @@

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Created with MultiQC
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Per Sequence Quality Scores - @@ -6580,7 +6743,7 @@

The number of reads with average quality scores. Shows if a subset of reads has poor quality.

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From the FastQC help:

The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a @@ -6592,14 +6755,17 @@

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Created with MultiQC
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Per Base Sequence Content - @@ -6627,7 +6793,7 @@

The proportion of each base position for which each of the four normal DNA bases has been called.

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To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot @@ -6668,13 +6834,13 @@

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Per Sequence GC Content - @@ -6701,7 +6867,7 @@

roughly normal distribution of GC content.

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From the FastQC help:

This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

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Created with MultiQC
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Per Base N Content - @@ -6762,7 +6931,7 @@

The percentage of base calls at each position for which an N was called.

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From the FastQC help:

If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the @@ -6777,14 +6946,17 @@

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Created with MultiQC
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Sequence Length Distribution

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Created with MultiQC
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Sequence Duplication Levels - @@ -6846,7 +7021,7 @@

The relative level of duplication found for every sequence.

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From the FastQC Help:

In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the @@ -6872,14 +7047,17 @@

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Created with MultiQC
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Overrepresented sequences by sample - @@ -6907,7 +7085,7 @@

The total amount of overrepresented sequences found in each library.

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FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as overrepresented.

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Top overrepresented sequences

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