homology_searched

A dataset containing the information of reads for homology search.

datasets

Clinical sequencing of tumor is usually performed on formalin-fixed
and paraffin-embedded samples and have many sequencing errors. We found that
the majority of these errors are detected in chimeric read caused by
single-strand DNA with micro-homology. Our filtering pipeline focuses on the
uneven distribution of the artifacts in each read and removes such errors in
formalin-fixed and paraffin-embedded samples without over-eliminating the
true mutations detected in fresh frozen samples.

Masachika Ikegami

MicroSEC

Sequence Error Filter for Formalin-Fixed and Paraffin-Embedded
Samples

homology_searched function

A list with 7 factors, each contains 1508 variables:<dl>
<dt>sample_name</dt>
<dd>sample name</dd><dt>Chr</dt>
<dd>altered chromosome</dd><dt>Pos</dt>
<dd>altered position</dd><dt>Ref</dt>
<dd>reference base</dd><dt>Alt</dt>
<dd>altered base</dd><dt>Direction</dt>
<dd>5' (pre) or 3' (post) sequence of the mutated base</dd><dt>Seq</dt>
<dd>sequence for homology search</dd>...</dl>

Format

An example sequence information file. — homology_searched

A list with 7 factors, each contains 1508 variables:<dl>
<dt>sample_name</dt>
<dd>sample name</dd>

<dt>Chr</dt>
<dd>altered chromosome</dd>

<dt>Pos</dt>
<dd>altered position</dd>

<dt>Ref</dt>
<dd>reference base</dd>

<dt>Alt</dt>
<dd>altered base</dd>

<dt>Direction</dt>
<dd>5' (pre) or 3' (post) sequence of the mutated base</dd>

<dt>Seq</dt>
<dd>sequence for homology search</dd>

...

</dl>

homology_searched: An example sequence information file.

Description

Usage

Arguments

Format