Tutorials

We currently offer a limited set of tutorials on various topics. If you have a nice idea or you wish to contribute a tutorial, let us know.

Tutorial: Getting started with NGS data

Getting started with NGS data

  1. Check out the load data page to learn how to load data and the list of supported data formats.
  2. Load the reference genome, typically a FASTA file. For improved speed, you may consider indexing these files
  3. Load a BAM file. This files needs to be sorted and indexed. Full BAM preparation instructions
  4. Create and load a coverage plot. Coverage plots give you a summary view of the sequencing data and are in many cases sufficient

Tutorial: Loading a MAF file from UCSC

This tutorial will guide you through the required steps to download a whole genome multiple alignment from the UCSC genome browser and explore it in GenomeView.

  1. Start GenomeView
  2. Load D. melanogaster genome from the Genome Explorer
  3. Load multiple alignment from UCSC
  4. done...

Start GenomeView

This should be self-explanatory, but in case it's not, you can check-out the Quick Start Guide

Load D. melanogaster genome from the Genome Explorer

What is the Genome Explorer?
You can find D. melanogaster genome in the insect tab. We'll need the dm3 release.
D. melanogaster (dm3) genome in the insect tab of the Genome ExplorerD. melanogaster (dm3) genome in the insect tab of the Genome Explorer

Load multiple alignment from UCSC

The URL for all multiple alignments for D. melanogaster is:
http://hgdownload.cse.ucsc.edu/goldenPath/dm3/multiz15way/

Copy the URL of one of the MAF files you find there, for example right click on chr2R.maf.gz which allows you to copy the URL to that file.

The full URL to that file is http://hgdownload.cse.ucsc.edu/goldenPath/dm3/multiz15way/chr2R.maf.gz

Make sure you copy this URL somewhere so you don't have to type it in a second.

Next tell GenomeView to load more data File > Load data..., select URL from the options. You now see a text field where you will paste the URL above.

Paste URL in the dialog box after selecting the URL option for loading data.Paste URL in the dialog box after selecting the URL option for loading data.

After you paste the URL, press OK

GenomeView will prompt you now whether you want to pre-process this file. You want to do that, so press yes.

Confirm you want to preprocess the MAF fileConfirm you want to preprocess the MAF file

GenomeView will now ask where the preprocessed files should be stored. Pick a location anywhere on your computer. If you want to load this multiple alignment in the future, you can directly those files from your local computer and you don't have to go through the steps here.

Once that's done, GenomeView will start processing the files, which can take a couple of minutes. This is a one-time process.

At the end GenomeView will load up the freshly produced multiple alignment.