Biomedical Engineering Reference
In-Depth Information
Summary of usage and operations of the
genomic_overlaps tool
Table 8.2
Operation
Description
count
Counts the number of overlapping test regions per
reference region
coverage
Calculates the depth coverage (i.e. the total number of
overlapping nucleotides) per reference region
density
Computes the density (i.e. the coverage divided by the
size of the reference region) of overlaps per reference
region
intersect
Computes the intersection between all pairs of test and
reference regions
offset
Computes the distances of test regions from their
overlapping reference regions
overlap
Finds the overlaps between all pairs of test and
reference regions
subset
Picks a subset of test regions depending on their
overlap with reference regions
operations and a variety of options for: (1) fi nding regions that match or
partially overlap; (2) counting the number of matches; (3) calculating
densities of matched regions; and (4) computing overlap offsets.
Applications include computation of gene expression from RNA-seq
data (e.g. RPKMs [30]), construction of average read profi les or heatmaps
across transcriptional start sites (TSSs), enrichment analyses of virtually
any genomic data set, such as genes of specifi c functional categories,
repeat types, single nucleotide polymorphisms (SNPs), or cancer-
associated regions.
8.3.3 The genomic_scans tool
The genomic_scans tool can be used for window-based computations
such as peak discovery. The command-line version offers several
parameters for controlling the window size, statistical tests, etc. Users
with basic C/C++ skills can easily modify the source code to perform the
statistical test of their choice using the GenomicRegionSetScanner
class described below.
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