<commit_before># RNA2DNA Usage

## Synopsis

### Graphical User Interface:

    RNA2DNA

### Command-line:

    RNA2DNA [options]

## Description



## Graphical User Interface

![Options](RNA2DNA1.png)

Click the help icon (question mark) at the top right of the GUI and
then an input field for help. Multiple files can be selected in the
file-browser using Ctrl-Click or Shift-Click. Fields can be reset to
their default values using the Reset button. Click OK to execute
RNA2DNA.

Additional GUI option tabs are documented below.

## Options

SNVs, -s SNVS, --snvs=SNVS

> Single-nucleotide-polymophisms (SNVs). Tabular and VCF format SNVs
> are supported. Supported tabular formats include `txt`, `tsv`, `csv`, `xlsx`,
> `xls`. Text files (`txt`) must have four whitespace separated columns
> representing the chromosome (CHROM), locus (POS), wild-type allele
> nucleotide (REF), and SNV nucleotide (ALT). Other tabular formats
> must provide CHROM, POS, REF, ALT headings. Extra values in tabular
> or VCF format files are mapped to the output. Required.

Read Alignment Files, -r ALIGNMENTS, --readalignments=ALIGNMENTS

> Read alignments files in indexed BAM format, with extension
> `.bam`. BAM index with extension `.bam.bai` must be located in the
> same directory. Required.

Output Folder, -o OUTPUT, --output=OUTPUT

> Output directory. Will be created if necessary. Files inside this directory will be overwritten by program output. Required. 

--version

>Show program's version number and exit. 

-h, --help

>Show program help and exit.

### Filtering

![Filtering](RNA2DNA2.png)

Exon Coords., -e EXONCOORDS, --exoncoords=EXONCOORDS

> Exon coordinates to filter out non-coding SNVs. See (Annotation Files)[Annotation.md] for format and download information. Optional.

### Read Counting

![Read Counting](RNA2DNA3.png)

Min. Reads, -m MINREADS, --minreads=MINREADS

> Minimum number of good reads at each SNV locus per alignment file. Default=10.   

Filter Alignments, -f, --alignmentfilter

> (Turn off) alignment filtering by length, edits, etc.

Unique Reads, -U, --uniquereads   

> Consider only distinct reads.  

Threads/BAm, -t TPB, --threadsperbam=TPB                   

> Worker threads per alignment file. Indicate no threading with 0. Default=1.

Quiet, -q, --quiet

> Do not show readCounts progress.

## See Also

[RNA2DNA Home](..), [Input Files](InputFiles.md), [Output Files](OutputFiles.md), [Annotation Files](AnnotationFiles.md)
<commit_msg>Documentation<commit_after># RNA2DNA Usage

## Synopsis

### Graphical User Interface:

    RNA2DNA
    RNA2DNA.py

### Command-line:

    RNA2DNA [options]
    RNA2DNA.py [options]

## Description

RNA2DNA evaluates evidence of allelic imbalance and asymmetry in next-gen
sequencing reads of exomes and RNA from normal and tumor samples from
the same individual.

## Graphical User Interface

![Options](RNA2DNA1.png)

Click the help icon (question mark) at the top right of the GUI and
then an input field for help. Multiple files can be selected in the
file-browser using Ctrl-Click or Shift-Click. Fields can be reset to
their default values using the Reset button. Click OK to execute
RNA2DNA.

Additional GUI option tabs are documented below.

## Options

SNVs, -s SNVS, --snvs=SNVS

> Single-nucleotide-polymophisms (SNVs). Tabular and VCF format SNVs
> are supported. Supported tabular formats include `txt`, `tsv`,
> `csv`, `xlsx`, `xls`. Text files (`txt`) must have four whitespace
> separated columns representing the chromosome (CHROM), locus (POS),
> wild-type allele nucleotide (REF), and SNV nucleotide (ALT). Other
> tabular formats must provide CHROM, POS, REF, ALT headings. Extra
> values in tabular or VCF format files are mapped to the output. See
> [Input Files](InputFiles.md) for more information. Required.

Read Alignment Files, -r ALIGNMENTS, --readalignments=ALIGNMENTS

> Read alignments files in indexed BAM format, with extension
> `.bam`. BAM index with extension `.bam.bai` must be located in the
> same directory. See [Input Files](InputFiles.md) for more
> information. Required.

Output Folder, -o OUTPUT, --output=OUTPUT

> Output directory. Will be created if necessary. Files inside this directory will be overwritten by program output. See [Output Files](OutputFiles.md) for more information on output files. Required. 

--version

>Show program's version number and exit. 

-h, --help

>Show program help and exit.

### Filtering

![Filtering](RNA2DNA2.png)

Exon Coords., -e EXONCOORDS, --exoncoords=EXONCOORDS

> Exon coordinates to filter out non-coding SNVs. See [Annotation Files](AnnotationFiles.md) for format and download information. Optional.

### Read Counting

![Read Counting](RNA2DNA3.png)

Min. Reads, -m MINREADS, --minreads=MINREADS

> Minimum number of good reads at each SNV locus per alignment file. Default=10.   

Filter Alignments, -f, --alignmentfilter

> (Turn off) alignment filtering by length, edits, etc.

Unique Reads, -U, --uniquereads   

> Consider only distinct reads.  

Threads/BAm, -t TPB, --threadsperbam=TPB                   

> Worker threads per alignment file. Indicate no threading with 0. Default=1.

Quiet, -q, --quiet

> Do not show readCounts progress.

### Filename Matching

![Filename Matching](RNA2DNA4.png)

Germline Exome, --normalexomere=NORMALEXOMERE

> Germline/Normal exome filename regular expression. Default: GDNA.

Normal Transcr., --normaltransre=NORMALTRANSRE 

> Normal transcriptome filename regular expression. Default: NRNA.

Somatic Exome, --tumorexomere=TUMOREXOMERE      

> Somatic/Tumor exome filename regular expression. Default: SDNA.

Tumor Transcr., --tumortransre=TUMORTRANSRE

> Tumor transcriptome filename regular expression. Default: TRNA.

### SNV Annotation

![SNV Annotation](RNA2DNA5.png)

Darned, -d DARNED, --darned=DARNED

> DARNED Annotations. See [Annotation Files](AnnotationFiles.md) for format and download information. Optional.  

Cosmic, -c COSMIC, --cosmic=COSMIC

> COSMIC Annotations. See [Annotation Files](AnnotationFiles.md) for format and download information. Optional.

## See Also

[RNA2DNA Home](..), [Input Files](InputFiles.md), [Output Files](OutputFiles.md), [Annotation Files](AnnotationFiles.md)

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