Biomedical Engineering Reference
In-Depth Information
can be combined into fairly elaborate scripts that can address a wide
range of issues during the course of a bioinformatics project.
In large-scale analyses it is important to avoid biases introduced by the
complexity and redundancy of large genome-wide data sets. For example,
when computing an average gene TSS profi le for ChIP-seq reads, it is
important to create a 'non-redundant' set of gene TSSs, which is not a
trivial task because gene transcripts with different identifi ers and possibly
originating in different databases may report slightly different TSSs for
transcripts that are in fact the same. The operations implemented in the
GenomicTools platform can help correct for these biases as a pre-
processing step before the actual computation takes place, or assess the
effect of the bias on the result.
8.3.1 The genomic_regions tool
The genomic_regions tool is designed to perform basic operations on
genomic region fi les. These are: (1) line-based operations, such as shifting,
shuffl ing, sorting, and modifying genomic regions; and (2) fi le-based
operations such as inverting or linking genomic regions. Table 8.1
comprises the complete list of operations and each operation is
documented in the user's manual, an entry of which is shown in Figure 8.3.
To get a list of options without the need to refer to the manual, simply
use the '-h' option.
$ genomic_regions shuffl e -h
$ genomic_regions shuffl e -h
USAGE:
genomic_regions shuffl e [OPTIONS] <REGION-SET>
USAGE:
genomic_regions shuffl e [OPTIONS] <REGION-SET>
DESCRIPTION:
Shuffl es intervals within given reference region-set.
DESCRIPTION:
Shuffl es intervals within given reference region-set.
DETAILS:
* Input formats: REG, GFF, BED, SAM
* Operand: interval
* Region requirements: single-interval
* Region-set requirements: none
DETAILS:
* Input formats: REG, GFF, BED, SAM
* Operand: interval
* Region requirements: single-interval
* Region-set requirements: none
OPTIONS:
--help
OPTIONS:
--help
help
help
[true]
[true]
-h
-h
help
help
[true]
[true]
-v
-v
verbose mode
verbose mode
[false]
[false]
-r
-r
reference region fi le
reference region fi le
[]
[]
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