{CSS} ScaleHD

ScaleHD - Automated Huntington Disease genotyping

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Job Label: {instance_label}

    {SAMPLE_LIST}

Welcome to ScaleHD!

You will find all your processed samples for {instance_label} on the left.


Click on a sample to the left in order to view the output for that sequence.

Clicking on subheadings will scroll you to the relevant section of ScaleHD output.


Help for navigating this output is found by clicking '?'. at the top right
Contact me with comments/questions/threats by pressing '@', also located at the top right.

If you wish to return to this landing page, you can click the ScaleHD version 'home button' at the top left.


Summary results for {instance_label}

Here's a brief summary of the genotyping results for this instance of ScaleHD.

Initially, you can see the summary table which displays sample genotypes and confidence. This table is filterable, with the dropdown headers.

If you wish to inspect a sample in greater detail, you can click the sample ID from the table, or from the list on the left.

Furthermore, you will find allele distribution graphs, for every allele successfully processed in this run of ScaleHD.


{ALLELETABLE}
Sample ID Allele 1 CAG size Allele 1 CCG size Allele 1 structure Allele 1 confidence Allele 2 CAG size Allele 2 CCG size Allele 2 structure Allele 2 confidence


ScaleHD Help

Here is where you can find an explanation about how to navigate this ScaleHD HTML output.


Layout

Upon opening the webpage, you are greeted by a grid-style layout. At the top left, the ScaleHD version utilised for your analysis acts as a 'home' button. Down the left-hand side of the webpage, you will find a list of samples that were processed during your run of ScaleHD. Within each sample entry, the three ScaleHD sub-stages are listed.


Along the top of the webpage, a header displays information about the currently-active sub-section. Additionally, contact and help links are persistent at the top right.


The remaining panel of the grid layout is the main content view, where data will be displayed. This panel will change to specific sample data when prompted by a mouse click.


Functionality

Landing page

Upon loading, you are welcomed by a landing page, which shows genotypes for all samples in the processed run, as well as general allele frequency distributions for the ScaleHD run.

Within the allele summary table, you will find an entry for each processed sample, and the resultant genotyping data from ScaleHD. You can click on the sample ID to view the sample page in more detail. This summary table can be filtered by utilising the dropdown menus at the top of each column. For allele confidence, you can filter by utilising filter operators. For example, \"<50\" would display only filters with a confidence less than 50 percent.

Further down the page are the summary graphs, displaying the distribution of CAG/CCG allele sizes present in the current instance of ScaleHD results. You can mouse over bins to see specific count values.


Sample navigation

On the left, you will find the list of samples processed by ScaleHD, and their subsequence sub-stage links. Clicking on a sample link will display the detailed sample results on the content view. The current sample activated will be highlighted in green, within this sample list; the same behaviour is present for selecting sub-stages. At the left of each sample ID, a small ASCII indicator will display whether a sample passed ScaleHD processing or not. This indicator is purely for informing the user whether samples could run all ScaleHD workflows without throwing exceptions, it does not guarantee anything in regards to genotyping confidence.


Sample details

Within a sample's detailed results page, the three sections of ScaleHD processing are displayed. First, Sequence quality control: a variety of statistics from FastQC are scraped and rendered within the browser. Sequence alignment utilises MSAViewer to render a sub-section of the sequence assembly for inspection. Genotyping results are displayed in two separate graphs: one for CCG and one for CAG sizes. The CAG distribution graph is zoom-able, allowing for the user to inspect potential expansions within a distribution, in more detail. Following this, SNP data is displayed in a few tables.

{SEQDATA}
{JAVASCRIPT}