Difference between revisions of "Create random track (analysis)"

Revision as of 18:14, 9 December 2020

Analysis title

Create random track

Provider

geneXplain GmbH

Class

RandomTrackExtractor

Plugin

com.genexplain.analyses (geneXplain analyses)

Create a track of randomly sampled genomic regions

Parameters

• Input track - Study track / Track with intervals of interest
• Sequence collection - Resource / Folder with sequences containing input track regions
• Species - Species of sequences in input track
• Standard chromosomes - Restrict sampling to standard chromosomes
• Sequence number - Number of sequences to sample
• Sample sequence length - Common length for sampled sequences
• Allow overlap - Allow sampled regions to overlap with regions in input track
• Output path - Path for output track with sampled regions
• Random number seed - Seed for random number generator

Description

This method creates a track of randomly sampled sequence regions, also called intervals, segments or subsequences. Upstream regions of genes serve as source for the random segments.

Sampling can take into account an input track in two ways. First, the lengths of output regions are sampled from lengths observed in the input track, so that the output track approximates the same length distribution. This behavior can be overridden by specifying a common sequence length, in which case all sampled sequences will have the same length.

Further, gene upstream regions that overlap with segments in the input track can be omitted from the sampling. Omission of overlapping upstream regions is active by default and can be switched off (see parameter description).

Specification of an input track is optional. Random seed and sequence length arguments with non-positive values are ignored. However, if no input track is provided, the sequence length argument is required.