GBROWSE TUTORIAL PDF

So, we will ignore those. This matters because the chromosome names occur in several places and serve to tie everything together. Now we start doing things. Past experience has taught that whenever you get a GFF3 file from elsewhere it is a darn fine idea to check that the reference sequence that all features are positioned on is defined at the top of the file.

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So, we will ignore those. This matters because the chromosome names occur in several places and serve to tie everything together. Now we start doing things. Past experience has taught that whenever you get a GFF3 file from elsewhere it is a darn fine idea to check that the reference sequence that all features are positioned on is defined at the top of the file.

To add reference sequence you need to know how long it is. Columns 2: Source: A comment that identifies where this feature came from or what it means 3: Type: Sequence Ontology term describing this feature 4, 5: Start position and end positions, 1 relative 6, 7, 8: Score, Strand, Phase 9: Attributes Name: used for searches and display Parent: Who this feature belongs to in a multi-part feature.

Genes are defined as mRNAs containing one or more exons, in this file. Displaying Human Data in GBrowse Now that we have our reference sequence and the Ensembl gene models for chromosomes 2 and 20, lets show them.

Create human. Click for more details. The default DB will be "annotations" - more on that in a bit What region and tracks GBrowse will show when it first comes up. What example regions will be displayed as hot links. Track default values. These can be overridden in each track.

Glyph determine how data is shown as a box, linked boxes, xyplot, Both the "dna" and "translation" glyphs are smart. They use semantic zooming to display information in different ways at high zoom and low zoom.

This track definition is more typical then the DNA and Translation tracks. GBrowse scans column 3 the Sequence Ontology term and only displays items with this feature type. The file also contains information on popups and hovering. This is leftover from the original yeast file. Create the Human Database In the human. When GBrowse runs, by default it will run as the same user as Apache.

GBrowse has many adaptors that it can use to get data with. This adaptor just reads files from a directory into memory and uses them there. However, to make it easier to keep track of what data was loaded, I like to create a new directory in the default location, and place data files there before loading them.

It helps me remember a week later what was uploaded. That means will load the data with a BioPerl script that uses that module to load it. From inside VMware, in Firefox type: To use a browser on your host system first type this command inside the VMware system: ifconfig Then type the inet addr into your browser.

In this case: You should see something like this: Play around with it a little. Enable different tracks, scroll and zoom in and out. If we had other annotation we wanted to show, we could add it incrementally from here. And we do! Lets show the example data that comes with SAMtools. File ex1. To try samtools, you may run the following commands: samtools faidx ex1.

Lets take a look at the SAM file. This script moves it back. Update 3 of them. Now we invoke some SAMtools magic. Save your changes, and hit the "[Reset]" link on your GBrowse window. This should return you to where you first started except that there is now a "Coverage xyplot " track you can turn on. Turn it on. Also, turn off "Cache Tracks". You want that off whenever you are experimenting with the configuration file. You should see something like: This shows the read coverage. We told GBrowse to flag any read depth below 20 as red.

You can also show read coverage with color intensity. You will now have a "Coverage density plot " track you can turn on. Showing Individual Reads You can also show the individual reads. It should look like: Zoom in. Showing Mapping Quality A lot of people want to show individual base read quality. We do this with a Perl callback, a short usually snippet of code that sets a parameter based on values in the feature.

The popup and hover settings in the file already use this. Give it a go. Showing Paired End Reads Finally, the example data is for paired end reads.

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OligoFinder Lets the user search for landmarks on the basis of unique mers or greater. PrimerDesigner Use primer3 to design PCR primers for features or target coordinates ProteinDumper Dump translated protein sequences in various formats RandomGene Generates random genes on the current view RestrictionAnnotator Creates restriction maps. SequenceDumper The same functionality as BatchDumper, but just shows features that overlap the current region on view. Spectrogram Reference sequences can be anything that acts as a convenient landmark: sequenced clones, contigs, scaffolds, golden path segments, or whole chromosomes.

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Using GBrowse 2.0 to visualize and share next-generation sequence data

Taum Email alerts New issue alert. Because installation of these dependencies can be tedious and confusing for the newcomer, GBrowse has recently been packaged in preconfigured virtual machines that can be run on the desktop or in the Amazon Cloud. Create a WIG file. Now that we have our reference sequence and the Ensembl gene models for chromosomes 2 and 20, lets show them. The process of setting up semantic options is a bit more interesting. Grouped Features In some circumstances you may wish to group features together to create a multipart feature. This is an extensive tutorial to take you through the main features and gotchas of configuring GBrowse as a server.

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