get_feature_seqs

This function is used to get the genomic features of interest
and the DNA sequences associated with them. This function takes advantage of
the <code>GenomicFeatures</code> package functions <code>threeUTRsByTranscript</code>,
<code>fiveUTRsByTranscript</code>, <code>exonsBy</code>, <code>intronsByTranscript</code>, and <code>cdsBy</code>. These
functions are used to generate the features given an input <code>tx.db</code> object. A
2bit <code>dna</code> input is also required for extracting features sequences.
The output of the this function is:<ul>
<li><code>$db</code>: the feature <code>GRanges</code> object</li>
<li><code>$seqs</code>: <code>DNAStringSet</code> of sequences associated to those features</li>
</ul>

On-target gene knockdown using siRNA ideally results from binding
fully complementary regions in mRNA transcripts to induce cleavage.
Off-target siRNA gene knockdown can occur through several modes, one being
a seed-mediated mechanism mimicking miRNA gene regulation. Seed-mediated
off-target effects occur when the ~8 nucleotides at the 5’ end of the guide
strand, called a seed region, bind the 3’ untranslated regions of mRNA,
causing reduced translation. Experiments using siRNA knockdown paired with
RNA-seq can be used to detect siRNA sequences with potential off-target
effects driven by the seed region. 'SeedMatchR' provides tools for exploring
and detecting potential seed-mediated off-target effects of siRNA in RNA-seq
experiments. 'SeedMatchR' is designed to extend current differential
expression analysis tools, such as 'DESeq2', by annotating results with
predicted seed matches. Using publicly available data, we demonstrate the
ability of 'SeedMatchR' to detect cumulative changes in differential gene
expression attributed to siRNA seed regions.

Tareian Cazares

SeedMatchR

Find Matches to Canonical SiRNA Seeds in Genomic Features

Gulcin Ozer

Jibo Wang

Rick Higgs

Eli Lilly and Company 

get_feature_seqs function

<dl><dt>tx.db</dt>
<dd>A tx.db object</dd>
<dt>dna</dt>
<dd>A 2bit dna sequence</dd>
<dt>feature.type</dt>
<dd>The type of feature to return. Options: 3UTR, 5UTR,
exons, introns, cds</dd></dl>

Arguments

Get transcripts features and feature sequences — get_feature_seqs

<dl>

<dt>tx.db</dt>
<dd>A tx.db object</dd>


<dt>dna</dt>
<dd>A 2bit dna sequence</dd>


<dt>feature.type</dt>
<dd>The type of feature to return. Options: 3UTR, 5UTR,
exons, introns, cds</dd>

</dl>

get_feature_seqs: Get transcripts features and feature sequences

Description

Usage

Value

Arguments

Examples