fun_hairpin_check

This function attempts to find hairpin structure sequences.

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

fun_hairpin_check function

<dl><dt>hairpin_seq_tmp</dt>
<dd>The sequence to be checked.</dd>
<dt>ref_seq</dt>
<dd>Reference sequence around the mutation.</dd>
<dt>hairpin_length</dt>
<dd>The temporal length of hairpin sequences.</dd>
<dt>hair</dt>
<dd>The length of sequences to be checked.</dd></dl>

Arguments

Hairpin-structure sequence check function — fun_hairpin_check

<dl>

<dt>hairpin_seq_tmp</dt>
<dd>The sequence to be checked.</dd>


<dt>ref_seq</dt>
<dd>Reference sequence around the mutation.</dd>


<dt>hairpin_length</dt>
<dd>The temporal length of hairpin sequences.</dd>


<dt>hair</dt>
<dd>The length of sequences to be checked.</dd>

</dl>

fun_hairpin_check: Hairpin-structure sequence check function

Description

Usage

Value

Arguments