public class RnaSeqMetrics extends MultilevelMetrics
Modifier and Type | Field | 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.
|
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_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.
|
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.
|
LIBRARY, READ_GROUP, SAMPLE
Constructor | Description |
---|---|
RnaSeqMetrics() |
public long PF_BASES
public long PF_ALIGNED_BASES
public Long RIBOSOMAL_BASES
public long CODING_BASES
public long UTR_BASES
public long INTRONIC_BASES
public long INTERGENIC_BASES
public long IGNORED_READS
public long CORRECT_STRAND_READS
public long INCORRECT_STRAND_READS
public Double PCT_RIBOSOMAL_BASES
public double PCT_CODING_BASES
public double PCT_UTR_BASES
public double PCT_INTRONIC_BASES
public double PCT_INTERGENIC_BASES
public double PCT_MRNA_BASES
public double PCT_USABLE_BASES
public double PCT_CORRECT_STRAND_READS
public double MEDIAN_CV_COVERAGE
public double MEDIAN_5PRIME_BIAS
public double MEDIAN_3PRIME_BIAS
public double MEDIAN_5PRIME_TO_3PRIME_BIAS