RNA2DNAlign Examples

• Command-line
• Graphical User Interface

Command-line:

Example 1: BAM files and single SNV file in TSV format.

cd RNA2DNAlign/data
../bin/RNA2DNAlign -r "example-*.bam" -s "example-SNV.tsv" -o example1

Example 2: BAM and VCF files for each dataset, exonic SNV filtering, and DARNED and COSMIC annotations using the supplied annotation files.

cd RNA2DNAlign/data
../bin/RNA2DNAlign -r "example-GDNA.bam example-NRNA.bam example-SDNA.bam example-TRNA.bam" -s "example-*.vcf" -o example2 -e UCSC_Human_hg19_RefSeq_CDS_exon_coordinates.txt -d DARNED_hg19.txt -c CosmicMutantExport_hg19.tsv.gz

Result files corresponding to this analysis are available in the RNA2DNAlign/data directory in the example-output directory.

Example output files:

• Events_LOH.tsv
• Events_RNAed.tsv
• Events_SOM.tsv
• Events_T-RNAed.tsv
• Events_T-VSE.tsv
• Events_T-VSL.tsv
• Events_VSE.tsv
• Events_VSL.tsv
• readCounts.tsv
• summary_result.txt

Example 3: BAM and VCF files for each dataset, exonic SNV filtering, and minimum reads per loci in each dataset of 3.

cd RNA2DNAlign/data
../bin/RNA2DNAlign -r "example-*.bam" -s "example-*.vcf" -o example3 -e UCSC_Human_hg19_RefSeq_CDS_exon_coordinates.txt -m 3

Graphical User Interface

Example 1: BAM files and single SNV file in TSV format.

1. Select the SNV file by clicking on the Browse button, navigating to RNA2DNAlign/data, selecting example-SNV.tsv, and clicking OK.

1. Select the BAM files by clicking on the Browse button, navigating to RNA2DNAlign/data, selecting all the BAM files, using shift-click or control-click as needed, and clicking OK.

1. Specify the output directory by clicking on the Browse button, navigating to RNA2DNAlign/data, clicking Create Folder, entering “example1”, and clicking Open.

1. Click OK to execute the program.

Example 2: BAM and VCF files for each dataset, exonic SNV filtering, and DARNED and COSMIC annotations using the supplied annotation files.

1. Select the VCF files by clicking on the Browse button, navigating to RNA2DNAlign/data, selecting all the VCF files, using shift-click or control-click as needed, and clicking OK.

1. Select the BAM files by clicking on the Browse button, navigating to RNA2DNAlign/data, selecting all the BAM files, using shift-click or control-click as needed, and clicking OK.

1. Specify the output directory by clicking on the Browse button, navigating to RNA2DNAlign/data, clicking Create Folder, entering “example2” and clicking Open.

1. Specify exonic SNV filtering by selecting the Filtering tab, clicking on the Browse button, navigating to RNA2DNAlign/data, selecting “UCSC_Human_hg19_RefSeq_CDS_exon_coordinates.txt”, and clicking OK.

1. Specify DARNED and COSMIC annotation of SNP events on the SNV Annotation tab, selecting the files DARNED_hg19.txt and CosmicMutantExport_hg19.tsv.gz.

2. Click OK to execute the program.

Result files corresponding to this analysis are available in the RNA2DNAlign/data directory in the example-output directory.

Example output files:

• Events_LOH.tsv
• Events_RNAed.tsv
• Events_SOM.tsv
• Events_T-RNAed.tsv
• Events_T-VSE.tsv
• Events_T-VSL.tsv
• Events_VSE.tsv
• Events_VSL.tsv
• readCounts.tsv
• summary_result.txt

See Also

RNA2DNAlign Home, Input Files, Output Files, Annotation Files