RNA2DNAlign Usage

Synopsis

Graphical User Interface:

RNA2DNAlign
RNA2DNAlign.py

Command-line:

RNA2DNAlign [options]
RNA2DNAlign.py [options]

Description

RNA2DNAlign evaluates evidence of allelic imbalance and asymmetry in next-gen sequencing reads of DNA and RNA from normal and tumor samples from the same individual.

Graphical User Interface

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-chooser using Ctrl-Click or Shift-Click. Fields can be reset to their default values using the Reset button. Click OK to execute RNA2DNAlign.

Additional GUI option tabs are documented below.

Options

SNVs, -s SNVS, –snvs=SNVS

Single-nucleotide-polymophisms (SNVs). Tabular and VCF format SNVs are supported. Multiple files are specified inside quotes, separated by spaces, and by using file globbing. See Input Files 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. Multiple files are specified inside quotes, separated by spaces, and by using file globbing. See Input Files 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 for more information on output files. Required.

–version

Show program’s version number and exit.

-h, –help

Show program help and exit.

Filtering

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

Exon coordinates to filter out non-exonic SNVs. Use of exon coordinates to filter the SNVs is strongly recommended for transcriptome-to-exome analyses. See Annotation Files for format and download information. Optional.

Read Counting

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

Germline DNA, –normaldnare=NORMALDNARE

Germline/Normal DNA filename regular expression. Default: GDNA.

Normal Transcr., –normaltransre=NORMALTRANSRE

Normal transcriptome filename regular expression. Default: NRNA.

Somatic DNA, –tumordnare=TUMORDNARE

Somatic/Tumor DNA filename regular expression. Default: SDNA.

Tumor Transcr., –tumortransre=TUMORTRANSRE

Tumor transcriptome filename regular expression. Default: TRNA.

SNV Annotation

Darned, -d DARNED, –darned=DARNED

DARNED Annotations. See Annotation Files for format and download information. Optional.

Cosmic, -c COSMIC, –cosmic=COSMIC

COSMIC Annotations. See Annotation Files for format and download information. Optional.

See Also

RNA2DNAlign Home, Input Files, Output Files, Annotation Files, Examples