RnaSeqMetrics (gatk 4.1.4.1 API)

java.lang.Object
- htsjdk.samtools.metrics.MetricBase
- - picard.metrics.MultilevelMetrics
  - - picard.analysis.RnaSeqMetrics

```
public class RnaSeqMetrics
extends MultilevelMetrics
```
Metrics about the alignment of RNA-seq reads within a SAM file to genes, produced by the CollectRnaSeqMetrics program and usually stored in a file with the extension ".rna_metrics".

Field Summary

Fields
Modifier and Type	Field and Description
`long`	`CODING_BASES` Number of bases in primary alignments that align to a non-UTR coding base for some gene, and not ribosomal sequence.
`long`	`CORRECT_STRAND_READS` Number of aligned reads that are mapped to the correct strand.
`long`	`IGNORED_READS` Number of primary alignments that are mapped to a sequence specified on command-line as IGNORED_SEQUENCE.
`long`	`INCORRECT_STRAND_READS` Number of aligned reads that are mapped to the incorrect strand.
`long`	`INTERGENIC_BASES` Number of bases in primary alignments that do not align to any gene.
`long`	`INTRONIC_BASES` Number of bases in primary alignments that align to an intronic base for some gene, and not a coding or UTR base.
`double`	`MEDIAN_3PRIME_BIAS` The median 3 prime bias of the 1000 most highly expressed transcripts, where 3 prime bias is calculated per transcript as: mean coverage of the 3 prime-most 100 bases divided by the mean coverage of the whole transcript.
`double`	`MEDIAN_5PRIME_BIAS` The median 5 prime bias of the 1000 most highly expressed transcripts.
`double`	`MEDIAN_5PRIME_TO_3PRIME_BIAS` The ratio of coverage at the 5 prime end to the 3 prime end based on the 1000 most highly expressed transcripts.
`double`	`MEDIAN_CV_COVERAGE` The median coefficient of variation (CV) or stdev/mean for coverage values of the 1000 most highly expressed transcripts.
`long`	`NUM_R1_TRANSCRIPT_STRAND_READS` The number of reads that support the model where R1 is on the strand of transcription and R2 is on the opposite strand.
`long`	`NUM_R2_TRANSCRIPT_STRAND_READS` The fraction of reads that support the model where R2 is on the strand of transcription and R1 is on the opposite strand.
`long`	`NUM_UNEXPLAINED_READS` The fraction of reads for which the transcription strand model could not be inferred.
`double`	`PCT_CODING_BASES` Fraction of PF_ALIGNED_BASES that mapped to protein coding regions of genes, CODING_BASES/PF_ALIGNED_BASES
`double`	`PCT_CORRECT_STRAND_READS` Fraction of reads corresponding to mRNA transcripts which map to the correct strand of a reference genome = CORRECT_STRAND_READS/(CORRECT_STRAND_READS + INCORRECT_STRAND_READS).
`double`	`PCT_INTERGENIC_BASES` Fraction of PF_ALIGNED_BASES that mapped to intergenic regions of genomic DNA, INTERGENIC_BASES/PF_ALIGNED_BASES
`double`	`PCT_INTRONIC_BASES` Fraction of PF_ALIGNED_BASES that correspond to gene introns, INTRONIC_BASES/PF_ALIGNED_BASES
`double`	`PCT_MRNA_BASES` Sum of bases mapped to regions corresponding to UTRs and coding regions of mRNA transcripts, PCT_UTR_BASES + PCT_CODING_BASES
`double`	`PCT_R1_TRANSCRIPT_STRAND_READS` The fraction of reads that support the model where R1 is on the strand of transcription and R2 is on the opposite strand.
`double`	`PCT_R2_TRANSCRIPT_STRAND_READS` The fraction of reads that support the model where R2 is on the strand of transcription and R1 is on the opposite strand.
`java.lang.Double`	`PCT_RIBOSOMAL_BASES` Fraction of PF_ALIGNED_BASES that mapped to regions encoding ribosomal RNA, RIBOSOMAL_BASES/PF_ALIGNED_BASES
`double`	`PCT_USABLE_BASES` The fraction of bases mapping to mRNA divided by the total number of PF bases, (CODING_BASES + UTR_BASES)/PF_BASES.
`double`	`PCT_UTR_BASES` Fraction of PF_ALIGNED_BASES that mapped to untranslated regions (UTR) of genes, UTR_BASES/PF_ALIGNED_BASES
`long`	`PF_ALIGNED_BASES` The total number of aligned PF bases.
`long`	`PF_BASES` The total number of PF bases including non-aligned reads.
`java.lang.Long`	`RIBOSOMAL_BASES` Number of bases in primary alignments that align to ribosomal sequence.
`long`	`UTR_BASES` Number of bases in primary alignments that align to a UTR base for some gene, and not a coding base.

Fields inherited from class picard.metrics.MultilevelMetrics
LIBRARY, READ_GROUP, SAMPLE

Constructor Summary

Constructors
Constructor and Description

RnaSeqMetrics()

Constructors
Constructor and Description
`RnaSeqMetrics()`

Method Summary
- Methods inherited from class htsjdk.samtools.metrics.MetricBase
  equals, hashCode, toString
- Methods inherited from class java.lang.Object
  clone, finalize, getClass, notify, notifyAll, wait, wait, wait

- Field Detail
  - PF_BASES
```
public long PF_BASES
```
    The total number of PF bases including non-aligned reads.
  - PF_ALIGNED_BASES
```
public long PF_ALIGNED_BASES
```
    The total number of aligned PF bases. Non-primary alignments are not counted. Bases in aligned reads that do not correspond to reference (e.g. soft clips, insertions) are not counted.
  - RIBOSOMAL_BASES
```
public java.lang.Long RIBOSOMAL_BASES
```
    Number of bases in primary alignments that align to ribosomal sequence.
  - CODING_BASES
```
public long CODING_BASES
```
    Number of bases in primary alignments that align to a non-UTR coding base for some gene, and not ribosomal sequence.
  - UTR_BASES
```
public long UTR_BASES
```
    Number of bases in primary alignments that align to a UTR base for some gene, and not a coding base.
  - INTRONIC_BASES
```
public long INTRONIC_BASES
```
    Number of bases in primary alignments that align to an intronic base for some gene, and not a coding or UTR base.
  - INTERGENIC_BASES
```
public long INTERGENIC_BASES
```
    Number of bases in primary alignments that do not align to any gene.
  - IGNORED_READS
```
public long IGNORED_READS
```
    Number of primary alignments that are mapped to a sequence specified on command-line as IGNORED_SEQUENCE. These are not counted in PF_ALIGNED_BASES, CORRECT_STRAND_READS, INCORRECT_STRAND_READS, or any of the base-counting metrics. These reads are counted in PF_BASES.
  - CORRECT_STRAND_READS
```
public long CORRECT_STRAND_READS
```
    Number of aligned reads that are mapped to the correct strand. 0 if library is not strand-specific.
  - INCORRECT_STRAND_READS
```
public long INCORRECT_STRAND_READS
```
    Number of aligned reads that are mapped to the incorrect strand. 0 if library is not strand-specific.
  - NUM_R1_TRANSCRIPT_STRAND_READS
```
public long NUM_R1_TRANSCRIPT_STRAND_READS
```
    The number of reads that support the model where R1 is on the strand of transcription and R2 is on the opposite strand.
  - NUM_R2_TRANSCRIPT_STRAND_READS
```
public long NUM_R2_TRANSCRIPT_STRAND_READS
```
    The fraction of reads that support the model where R2 is on the strand of transcription and R1 is on the opposite strand.
  - NUM_UNEXPLAINED_READS
```
public long NUM_UNEXPLAINED_READS
```
    The fraction of reads for which the transcription strand model could not be inferred.
  - PCT_R1_TRANSCRIPT_STRAND_READS
```
public double PCT_R1_TRANSCRIPT_STRAND_READS
```
    The fraction of reads that support the model where R1 is on the strand of transcription and R2 is on the opposite strand. For unpaired reads, it is the fraction of reads that are on the transcription strand (out of all the reads).
  - PCT_R2_TRANSCRIPT_STRAND_READS
```
public double PCT_R2_TRANSCRIPT_STRAND_READS
```
    The fraction of reads that support the model where R2 is on the strand of transcription and R1 is on the opposite strand. For unpaired reads, it is the fraction of reads that are on opposite strand than that of the the transcription strand (out of all the reads).
  - PCT_RIBOSOMAL_BASES
```
public java.lang.Double PCT_RIBOSOMAL_BASES
```
    Fraction of PF_ALIGNED_BASES that mapped to regions encoding ribosomal RNA, RIBOSOMAL_BASES/PF_ALIGNED_BASES
  - PCT_CODING_BASES
```
public double PCT_CODING_BASES
```
    Fraction of PF_ALIGNED_BASES that mapped to protein coding regions of genes, CODING_BASES/PF_ALIGNED_BASES
  - PCT_UTR_BASES
```
public double PCT_UTR_BASES
```
    Fraction of PF_ALIGNED_BASES that mapped to untranslated regions (UTR) of genes, UTR_BASES/PF_ALIGNED_BASES
  - PCT_INTRONIC_BASES
```
public double PCT_INTRONIC_BASES
```
    Fraction of PF_ALIGNED_BASES that correspond to gene introns, INTRONIC_BASES/PF_ALIGNED_BASES
  - PCT_INTERGENIC_BASES
```
public double PCT_INTERGENIC_BASES
```
    Fraction of PF_ALIGNED_BASES that mapped to intergenic regions of genomic DNA, INTERGENIC_BASES/PF_ALIGNED_BASES
  - PCT_MRNA_BASES
```
public double PCT_MRNA_BASES
```
    Sum of bases mapped to regions corresponding to UTRs and coding regions of mRNA transcripts, PCT_UTR_BASES + PCT_CODING_BASES
  - PCT_USABLE_BASES
```
public double PCT_USABLE_BASES
```
    The fraction of bases mapping to mRNA divided by the total number of PF bases, (CODING_BASES + UTR_BASES)/PF_BASES.
  - PCT_CORRECT_STRAND_READS
```
public double PCT_CORRECT_STRAND_READS
```
    Fraction of reads corresponding to mRNA transcripts which map to the correct strand of a reference genome = CORRECT_STRAND_READS/(CORRECT_STRAND_READS + INCORRECT_STRAND_READS). 0 if library is not strand-specific.
  - MEDIAN_CV_COVERAGE
```
public double MEDIAN_CV_COVERAGE
```
    The median coefficient of variation (CV) or stdev/mean for coverage values of the 1000 most highly expressed transcripts. Ideal value = 0.
  - MEDIAN_5PRIME_BIAS
```
public double MEDIAN_5PRIME_BIAS
```
    The median 5 prime bias of the 1000 most highly expressed transcripts. The 5 prime bias is calculated per transcript as: mean coverage of the 5 prime-most 100 bases divided by the mean coverage of the whole transcript.
  - MEDIAN_3PRIME_BIAS
```
public double MEDIAN_3PRIME_BIAS
```
    The median 3 prime bias of the 1000 most highly expressed transcripts, where 3 prime bias is calculated per transcript as: mean coverage of the 3 prime-most 100 bases divided by the mean coverage of the whole transcript.
  - MEDIAN_5PRIME_TO_3PRIME_BIAS
```
public double MEDIAN_5PRIME_TO_3PRIME_BIAS
```
    The ratio of coverage at the 5 prime end to the 3 prime end based on the 1000 most highly expressed transcripts.
- Constructor Detail
  - RnaSeqMetrics
```
public RnaSeqMetrics()
```

Class RnaSeqMetrics

Field Summary

Fields inherited from class picard.metrics.MultilevelMetrics

Constructor Summary

Method Summary

Methods inherited from class htsjdk.samtools.metrics.MetricBase

Methods inherited from class java.lang.Object

Field Detail

PF_BASES

PF_ALIGNED_BASES

RIBOSOMAL_BASES

CODING_BASES

UTR_BASES

INTRONIC_BASES

INTERGENIC_BASES

IGNORED_READS

CORRECT_STRAND_READS

INCORRECT_STRAND_READS

NUM_R1_TRANSCRIPT_STRAND_READS

NUM_R2_TRANSCRIPT_STRAND_READS

NUM_UNEXPLAINED_READS

PCT_R1_TRANSCRIPT_STRAND_READS

PCT_R2_TRANSCRIPT_STRAND_READS

PCT_RIBOSOMAL_BASES

PCT_CODING_BASES

PCT_UTR_BASES

PCT_INTRONIC_BASES

PCT_INTERGENIC_BASES

PCT_MRNA_BASES

PCT_USABLE_BASES

PCT_CORRECT_STRAND_READS

MEDIAN_CV_COVERAGE

MEDIAN_5PRIME_BIAS

MEDIAN_3PRIME_BIAS

MEDIAN_5PRIME_TO_3PRIME_BIAS

Constructor Detail

RnaSeqMetrics