Skip to content

Usage

Jump to bottom
kevinkovalchik edited this page Oct 1, 2021 · 6 revisions

Running MhcVizPipe

Running an analysis (see numbered figure below):

  1. Load data by pasting a peptide list into the peptide list section, using the "drag and drop" area, or clicking "Select a File". Note: You may load more than one file at a time. If you do so the sample names will be completed using the filenames and all samples will be automatically added to the analysis. You can skip steps 2 and 3 unless you are adding other individual samples.

  2. Enter a sample name and (optionally) a description of the sample. If you selected a single file the filename will have been automatically entered into the sample name field, but you are free to change it.

  3. Click the "LOAD DATA" button and the sample will show up in the table under "Loaded data".

  4. Add more samples as needed by repeating steps 1-3.

  5. Using the drop-down "MHC class" menu, select the class of peptides you are analyzing (i.e. class I or class II).

  6. Add alleles using the "Alleles" search box.

    • Start typing an allele name and available options will appear. Note that the format you enter must match the available list, so pay attention to how the allele names are formatted. You can choose up to six alleles.
    • Once you have chosen the alleles for a sample, select the "allele" cell in for that sample in the table and click the arrow button to the left of the allele search box to add those alleles to the sample.
    • You can select more than one sample using the shift key. This way you can add alleles to more than one sample at a time, if they share alleles.

  7. Optionally, use the text boxes above the "GO!" button to enter a general description of the experiment and your name (if needed for your own bookkeeping).

  8. Optionally, add some experimental information in the "Experimental Information" text area. Some possible fields are provided for you. Type the information in to the right of the colons. If you have something else you would like to add, just enter it in the same format (i.e. field name : info). Any of the example fields that don't have information added to them won't be displayed in the report

  9. Click the "GO!" button to start your analysis. You will see a loading screen while things are running, followed by a pop-up window with a link to the report and figures.

Clone this wiki locally