RNA2DNAlign Output Files

RNA2DNAlign output files are created in the directory specified. The folder will be created if necessary. Existing files will be overwritten.

Summary

The summary_result.txt file summarizes the count of each type of event observed.

See example output files in the RNA2DNAlign/data directory.

Event Files

Each execution of RNA2DNAlign will create (up to) eight tab-separated value event files representing the following events: RNA editing (Events_RNAed.tsv), tumor-specific RNA editing (Events_T-RNAed.tsv), variant-specific expression (Events_VSE.tsv) or loss (Events_VSL.tsv), tumor-specific variant expression (Events_T-VSE.tsv) or loss (Events_T-VSL.tsv), somatic mutagenesis (Events_SOM.tsv), and loss of heterozygosity (Events_LOH.tsv).

See example output files in the RNA2DNAlign/data/example-output directory.

Event File Fields

AlignedReads

Name of the aligned reads file for the following read counts.

CHROM

Chromosome identifier

POS

Chromosome position of the variant

REF

Reference allele nucleotide

ALT

Variant allele nucleotide

SNPCountForward

Number of forward oriented variant reads in the paired end alignment.

SNPCountReverse

Number of reverse oriented variant reads in the paired end alignment.

RefCountForward

Number of forward oriented reference reads in the paired end alignment.

RefCountReverse

Number of reverse oriented reference reads in the paired end alignment.

SNPCount

Total number of variant reads.

RefCount

Total number of reference reads.

R

Proportion of variant reads.

HomoVarSc

Score of locus as homozygous variant.

HetSc

Score of locus as heterozygous reference and variant.

HomoRefSc

Score of locus as homozygous reference.

VarDomSc

Score of locus as dominant for the variant allele.

RefDomSc

Score of locus as dominant for the reference allele.

NotHomoVarpV

p-Value of read counts with respect to homozygous variant null model.

NotHomoRefpV

p-Value of read counts with respect to homozygous reference null model.

NotHetpV

p-Value of read counts with respect to heterozygous reference and variant null model.

VarDompV

p-Value of increased variant read counts with respect to heterozygous reference and variant null model.

RefDompV

p-Value of increased reference read counts with respect to heterozygous reference and variant null model.

NotHomoVarFDR

Multiple-test corrected FDR significance of read counts with respect to homozygous variant null model.

NotHomoRefFDR

Multiple-test corrected FDR significance of read counts with respect to homozygous reference null model.

NotHetFDR

Multiple-test corrected FDR significance of read counts with respect to heterozygous reference and variant null model.

VarDomFDR

Multiple-test corrected FDR significance of increased variant read counts with respect to heterozygous reference and variant null model.

RefDomFDR

Multiple-test corrected FDR significance of increased reference read counts with respect to heterozygous reference and variant null model.

Read Counts

A tab-separated values file consisting of the computed read-counts is also provided (readCounts.tsv). This file contains the read counts for each SNV locus in each BAM file and computes the various statistical tests described above, in “Event File Fields”. The read counts file can be used to investigate the computed values for expected events that didn’t pass filtering, significance, or scoring thresholds.

See Also

RNA2DNAlign Home, Usage, Input Files, Annotation Files, Examples