RnaSeqMetrics (PICARD JDK API Documentation)

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 aligments that align to a non-UTR coding base for some gene, and not ribosomal sequence.
`long`	`CORRECT_STRAND_READS` Number of aligned reads that map to the correct strand.
`long`	`IGNORED_READS` Number of primary alignments that map to a sequence specified on command-line as IGNORED_SEQUENCE.
`long`	`INCORRECT_STRAND_READS` Number of aligned reads that map to the incorrect strand.
`long`	`INTERGENIC_BASES` Number of bases in primary aligments that do not align to any gene.
`long`	`INTRONIC_BASES` Number of bases in primary aligments 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' 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, where 5 prime bias is calculated per transcript as: mean coverage of the 5' most 100 bases divided by the mean coverage of the whole transcript.
`double`	`MEDIAN_5PRIME_TO_3PRIME_BIAS` The ratio of coverage at the 5' end of to the 3' end based on the 1000 most highly expressed transcripts.
`double`	`MEDIAN_CV_COVERAGE` The median CV of coverage of the 1000 most highly expressed transcripts.
`double`	`PCT_CODING_BASES` CODING_BASES / PF_ALIGNED_BASES
`double`	`PCT_CORRECT_STRAND_READS` CORRECT_STRAND_READS/(CORRECT_STRAND_READS + INCORRECT_STRAND_READS).
`double`	`PCT_INTERGENIC_BASES` INTERGENIC_BASES / PF_ALIGNED_BASES
`double`	`PCT_INTRONIC_BASES` INTRONIC_BASES / PF_ALIGNED_BASES
`double`	`PCT_MRNA_BASES` PCT_UTR_BASES + PCT_CODING_BASES
`java.lang.Double`	`PCT_RIBOSOMAL_BASES` RIBOSOMAL_BASES / PF_ALIGNED_BASES
`double`	`PCT_USABLE_BASES` The percentage of bases mapping to mRNA divided by the total number of PF bases.
`double`	`PCT_UTR_BASES` 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 aligments that align to ribosomal sequence.
`long`	`UTR_BASES` Number of bases in primary aligments 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 aligments that align to ribosomal sequence.
  - CODING_BASES
```
public long CODING_BASES
```
    Number of bases in primary aligments 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 aligments 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 aligments 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 aligments that do not align to any gene.
  - IGNORED_READS
```
public long IGNORED_READS
```
    Number of primary alignments that map 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 map to the correct strand. 0 if library is not strand-specific.
  - INCORRECT_STRAND_READS
```
public long INCORRECT_STRAND_READS
```
    Number of aligned reads that map to the incorrect strand. 0 if library is not strand-specific.
  - PCT_RIBOSOMAL_BASES
```
public java.lang.Double PCT_RIBOSOMAL_BASES
```
    RIBOSOMAL_BASES / PF_ALIGNED_BASES
  - PCT_CODING_BASES
```
public double PCT_CODING_BASES
```
    CODING_BASES / PF_ALIGNED_BASES
  - PCT_UTR_BASES
```
public double PCT_UTR_BASES
```
    UTR_BASES / PF_ALIGNED_BASES
  - PCT_INTRONIC_BASES
```
public double PCT_INTRONIC_BASES
```
    INTRONIC_BASES / PF_ALIGNED_BASES
  - PCT_INTERGENIC_BASES
```
public double PCT_INTERGENIC_BASES
```
    INTERGENIC_BASES / PF_ALIGNED_BASES
  - PCT_MRNA_BASES
```
public double PCT_MRNA_BASES
```
    PCT_UTR_BASES + PCT_CODING_BASES
  - PCT_USABLE_BASES
```
public double PCT_USABLE_BASES
```
    The percentage of bases mapping to mRNA divided by the total number of PF bases.
  - PCT_CORRECT_STRAND_READS
```
public double PCT_CORRECT_STRAND_READS
```
    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 CV of coverage 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, where 5 prime bias is calculated per transcript as: mean coverage of the 5' 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' 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' end of to the 3' 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

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