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doc:interval

Create single interval

Tool version

1.0.0

Keywords

BED format

Summary

Creates a single genomic interval. Output will be in BED format.

Description

This tool creates an interval file (BED6 format) with one entry. BED format is a tab-separated format which is used to describe a genomic interval. BED files can be uploaded into genome browsers. For more details, check the BED format in the UCSC website.

General comments (Warning/Tips)

Once the newly generated dataset appears in the history, you must select which genome it belongs to by editing the attributes. To do so, click on the pencil icon in the history item.

In the history item, you can click on a direct link (display at UCSC main) to display the interval in UCSC genome browser.

Input

  • Chromosome: enter the name of the chromosome (or scaffold).
  • Start position: in this field, write the starting position of the feature in the chromosome. In genome browsers such as UCSC chromosome position numbering starts at 0. Depending on the downstream analysis you want to perform, you may need to subtract the value 1 to refer to the desired position.
  • End position: enter the ending position of the feature in the chromosome.
  • Name: enter the name of the feature. This field is optional. The name can be displayed in the genome browser window. If you don't enter a name, other tools may not work with the resulting genomic interval.
  • Strand: select the strand: 'plus' or 'minus'. Default value is 'plus'.

Output

The output is a dataset of type BED with one entry.

Example

Input

Chromosome: chr7

Start position: 5247945

End position: 5248650

Name: Clone_A

Strand: plus

Output

Edited on

July 15th, 2014

doc/interval.txt · Last modified: 2014/11/28 17:00 by slegras