CombinedAlignment

A 'shiny' app that supports both dual and bulk RNA-seq, with the dual
RNA-seq functionality offering the flexibility to perform either a
sequential approach (where reads are mapped separately to each genome)
or a combined approach (where reads are aligned to a single merged
genome). The user-friendly interface automates the analysis process,
providing step-by-step guidance, making it easy for users to navigate
between different analysis steps, and download intermediate results
and publication-ready plots.

Carmine Fruggiero

inDAGO

A GUI for Dual and Bulk RNA-Sequencing Analysis

Gaetano Aufiero

CombinedAlignment function

<dl><dt>lalista</dt>
<dd>list of samples</dd>
<dt>nodes</dt>
<dd>logic cores</dd>
<dt>readsPath</dt>
<dd>sample folders</dd>
<dt>GenomeConcIndex</dt>
<dd>genome index</dd>
<dt>outBam</dt>
<dd>output folder</dd>
<dt>threads</dt>
<dd>processes</dd>
<dt>outFormat</dt>
<dd>BAM or SAM</dd>
<dt>phredScore</dt>
<dd>quality score</dd>
<dt>maxExtractedSubreads</dt>
<dd>number of subreads</dd>
<dt>consensusVote</dt>
<dd>consensus</dd>
<dt>mismatchMax</dt>
<dd>mismatch</dd>
<dt>uniqueOnly</dt>
<dd>no multimapping</dd>
<dt>maxMultiMapped</dt>
<dd>multimapping</dd>
<dt>indelLength</dt>
<dd>indel</dd>
<dt>fragmentMinLength</dt>
<dd>fragment minumum length</dd>
<dt>fragmentMaxLength</dt>
<dd>fragment maximum length</dd>
<dt>matesOrientation</dt>
<dd>mate orientation</dd>
<dt>readOrderConserved</dt>
<dd>read order</dd>
<dt>coordinatesSorting</dt>
<dd>sorting</dd>
<dt>allJunctions</dt>
<dd>junctions</dd>
<dt>tempfolder</dt>
<dd>temporary folder</dd>
<dt>readsAlignedBlock</dt>
<dd>chunks</dd></dl>

Arguments

Title — CombinedAlignment

<dl>

<dt>lalista</dt>
<dd>list of samples</dd>


<dt>nodes</dt>
<dd>logic cores</dd>


<dt>readsPath</dt>
<dd>sample folders</dd>


<dt>GenomeConcIndex</dt>
<dd>genome index</dd>


<dt>outBam</dt>
<dd>output folder</dd>


<dt>threads</dt>
<dd>processes</dd>


<dt>outFormat</dt>
<dd>BAM or SAM</dd>


<dt>phredScore</dt>
<dd>quality score</dd>


<dt>maxExtractedSubreads</dt>
<dd>number of subreads</dd>


<dt>consensusVote</dt>
<dd>consensus</dd>


<dt>mismatchMax</dt>
<dd>mismatch</dd>


<dt>uniqueOnly</dt>
<dd>no multimapping</dd>


<dt>maxMultiMapped</dt>
<dd>multimapping</dd>


<dt>indelLength</dt>
<dd>indel</dd>


<dt>fragmentMinLength</dt>
<dd>fragment minumum length</dd>


<dt>fragmentMaxLength</dt>
<dd>fragment maximum length</dd>


<dt>matesOrientation</dt>
<dd>mate orientation</dd>


<dt>readOrderConserved</dt>
<dd>read order</dd>


<dt>coordinatesSorting</dt>
<dd>sorting</dd>


<dt>allJunctions</dt>
<dd>junctions</dd>


<dt>tempfolder</dt>
<dd>temporary folder</dd>


<dt>readsAlignedBlock</dt>
<dd>chunks</dd>

</dl>

CombinedAlignment: Title

Description

Usage

Arguments