Tutorials

All of our workbenches are based on the same user interface. By going through the four basic tutorials you will get more out of our software in the fastest and smoothest way.

The additional tutorials introduce more advanced features of the workbenches, of which some are only available in our commercial workbenches: CLC RNA Workbench, CLC DNA Workbench, CLC Protein Workbench, and CLC Main Workbench.

Please note that the tutorials are based on Sequence Viewer 4 and Main Workbench 3.

Some tutorials are based on CLC bio's set of example data.

	Basic tutorials	Movie	Download
	Getting started This tutorial will show you how to navigate the user interface, how to create folders, and how to import data.	3:23	5 pages
	Opening a DNA sequence A brief tutorial showing how to open a DNA sequence in the CLC Workbenches.	3:54	3 pages
	Adjust and save view settings This tutorial shows you how to adjust view settings, e.g. which restriction sites to display on your sequence, and also how to save the settings.	3:20	4 pages
	GenBank search and download This tutorial will teach you how to search, how to save your searches, and about matching objects.	3:30	3 pages

	High-throughput analysis	Movie	Download
	Small RNA analysis Small RNA analysis using Illumina data.		14 pages
	RNA-seq analysis - Part I First part of a series of tutorials about RNA-seq.		8 pages
	RNA-seq analysis - Part II Non-specific matches and expression measures.		9 pages
	RNA-seq analysis - Part III Exon discovery.		4 pages
	RNA-seq analysis - Part IV Spikes and quality control.		8 pages
	To come: RNA-seq analysis - Part V Differential expression and annotation tests.
	Resequencing This tutorial shows a typical resequencing work flow including data import, read mapping and SNP/DIP detection		8 pages
	De novo sequencing Learn how to import data, perform de novo assembly and run a batch BLAST analysis of the results		6 pages
	Read mapping in details In this tutorial, you will learn what the parameters for mapping reads to a reference mean, and you will hopefully end up being able to make better decisions about the analysis of your own data.		10 pages
	ChIP-seq basics Learn the full ChIP-seq work flow from importing data, running read mapping and peak detection and finally inspect the results.		6 pages
	ChIP-Seq: understanding the details Learn the details on how to adjust parameters for peak finding in ChIP-Seq data, and see examples of how to interpret results.		6 pages
	Expression analysis - Part I Getting started		6 pages
	Expression analysis - Part II Quality control		7 pages
	Expression analysis - Part III Differentially expressed genes		6 pages
	Expression analysis - Part IV Annotation test		4 pages

	Additional tutorials	Movie	Download
	Assembly Learn how to assemble trace files and edit the contigs.	12:37	5 pages
	Cloning I In silico cloning part I - finding the right enzymes	6:09	5 pages
	Cloning II In silico cloning part II - inserting the fragment	6:20	4 pages
	Primer design This tutorial will show you a flexible and quick way of finding specific primers.	8:29	5 pages
	BLAST This tutorial will teach you how to perform a BLAST search and download related sequences.	4:46	4 pages
	Aligning sequences Learn how to align sequences and viewing alignments.	2:09	3 pages
	Working with sequence lists Sequence lists provide an easy way of working with many sequences at a time. This tutorial will show you how to easily add and remove sequence from a list.	1:56
	BLAST tips: Locate a protein sequence on the chromosome. Learn how to use BLAST to locate the gene of a protein sequence on the chromosome.	6:17	6 pages
	Working with annotations This tutorial will show you how to show, browse, search for, add, edit and copy annotations.	7:35	6 pages
	Simple RNA folding Learn the basics of folding RNA molecules including modifying the layout.	4:55	4 pages
	Partition function Learn how to calculate partition function, and see how to color bases according to paired and un-paired probabilities.	2:54
	Alignment-based primer design Learn how to design degenerate primers for PCR amplification of sequences in an alignment. Right click here - to download the alignment used in this tutorial.	4:42
	Detect restriction site Learn how to detect and view restriction sites.		4 pages
	Create and modify a phylogenetic tree Learn how to create a phylogenetic tree from an existing alignment.		2 pages
	Proteolytic cleavage detection This tutorial will teach you how to find and view proteolytic cleavage sites.		3 pages