A BED (Browser Extensible Data) file is a special case of a region list: it is a tab-delimited text file and the first three columns of BED files contain the chromosome, start, and stop locations. To import a bed file to be used as a data region list, follow the import instructions for region lists. A BED File might also be visualized as an annotation file containing regions in the Genome Browser. 

Using a BED file as an annotation source for the genome browser

BED files do not contain individual sequences nor do the regions have names. For instance, the UCSC table browser has a BED file that contains reads from a long non-coding RNA-Seq experiment and you might like to view this information in the context of your dataset. Before you could visualize a BED file in the chromosome viewer, you would have to create a Partek annotation file from the BED file.

• From the top command menu, select Tools > Annotation Manager
• In the My Annotations tab, select Create Annotation
• Select BED file (.bed) under Choose Annotation Type

• Under File Locations, specify the Source (input BED file) with the Browse menu item.  You may also specify the Result file name (of the annotation file) and location with the Browse button. You might consider saving the result file to your Microarray Libraries folder

• In the Annotation Details section of the dialog box, specify the Name of the annotation database that will be visible from within Genomics Suite, Species, and Genome Build. Preview Chromosome Names would be used if the chromosome names in the annotation file must be changed to match the name of the chromosome in the genomic annotations. 

• Select OK

Visualizing a BED file as an annotation track in the genome browser

In order to use a BED file as an Annotation track in the Genome Browser, first create the annotation file as described above, being careful to have specified the species and genome build appropriately.

• Invoke the Genome Browser by right-clicking in any spreadsheet that has genomic features on rows (gene lists, ANOVA results, SNP detection) and select either Browse to Row or Browse to Location

• In the Track Toolbar on the left, select New Track which invokes the dialog shown in Figure 21

• Select Add an annotation track with genomic features from a selected annotation source and select Next

• Next you will have to choose the annotation file that was created from the BED file. The  procedure for doing this might vary slightly depending on the type of spreadsheet you have displayed in the Genome Browser. You may be shown a list of annotations that includes the annotation source you have created; in this case, select the radio button in the Available Annotations panel. If, however,

• At the bottom of the screen, you should either check or uncheck the box next to Separate strands (checking means that the BED file contained the strand information for each region and you wish to visualize the regions on different strands). Unselecting Separate strands should be used if the BED file did not contain strand information or if you do not wish to display the information on separate strands. Select Create.

Your Rating:

Thanks for voting!

Please Wait

Results:

0

rates