Package picard.analysis
Class RnaSeqMetrics
java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.metrics.MultilevelMetrics
picard.analysis.RnaSeqMetrics
@DocumentedFeature(groupName="Metrics",
summary="Metrics")
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".
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Field Summary
FieldsModifier and TypeFieldDescriptionlong
Number of bases in primary alignments that align to a non-UTR coding base for some gene, and not ribosomal sequence.long
Number of aligned reads that are mapped to the correct strand.long
Number of primary alignments that are mapped to a sequence specified on command-line as IGNORED_SEQUENCE.long
Number of aligned reads that are mapped to the incorrect strand.long
Number of bases in primary alignments that do not align to any gene.long
Number of bases in primary alignments that align to an intronic base for some gene, and not a coding or UTR base.double
The median 3 prime bias of the 1000 most highly expressed transcripts that have a length greater than the END_BIAS_BASES parameter, where 3 prime bias is calculated per transcript as: mean coverage of the 3 prime-most number of bases, divided by the mean coverage of the whole transcript.double
The median 5 prime bias of the 1000 most highly expressed transcripts that have a length greater than the END_BIAS_BASES parameter.double
The ratio of coverage at the 5 prime end to the 3 prime end based on the 1000 most highly expressed transcripts that have a length greater than the END_BIAS_BASES parameter.double
The median coefficient of variation (CV) or stdev/mean for coverage values of the 1000 most highly expressed transcripts that have a length greater than the END_BIAS_BASES parameter.long
The number of reads that support the model where R1 is on the strand of transcription and R2 is on the opposite strand.long
The fraction of reads that support the model where R2 is on the strand of transcription and R1 is on the opposite strand.long
The fraction of reads for which the transcription strand model could not be inferred.double
Fraction of PF_ALIGNED_BASES that mapped to protein coding regions of genes, CODING_BASES/PF_ALIGNED_BASESdouble
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
Fraction of PF_ALIGNED_BASES that mapped to intergenic regions of genomic DNA, INTERGENIC_BASES/PF_ALIGNED_BASESdouble
Fraction of PF_ALIGNED_BASES that correspond to gene introns, INTRONIC_BASES/PF_ALIGNED_BASESdouble
Sum of bases mapped to regions corresponding to UTRs and coding regions of mRNA transcripts, PCT_UTR_BASES + PCT_CODING_BASESdouble
The fraction of reads that support the model where R1 is on the strand of transcription and R2 is on the opposite strand.double
The fraction of reads that support the model where R2 is on the strand of transcription and R1 is on the opposite strand.Fraction of PF_ALIGNED_BASES that mapped to regions encoding ribosomal RNA, RIBOSOMAL_BASES/PF_ALIGNED_BASESdouble
The fraction of bases mapping to mRNA divided by the total number of PF bases, (CODING_BASES + UTR_BASES)/PF_BASES.double
Fraction of PF_ALIGNED_BASES that mapped to untranslated regions (UTR) of genes, UTR_BASES/PF_ALIGNED_BASESlong
The total number of aligned PF bases.long
The total number of PF bases including non-aligned reads.Number of bases in primary alignments that align to ribosomal sequence.long
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
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Constructor Summary
Constructors -
Method Summary
Methods inherited from class htsjdk.samtools.metrics.MetricBase
equals, hashCode, toString
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Field Details
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PF_BASES
public long PF_BASESThe total number of PF bases including non-aligned reads. -
PF_ALIGNED_BASES
public long PF_ALIGNED_BASESThe 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
Number of bases in primary alignments that align to ribosomal sequence. -
CODING_BASES
public long CODING_BASESNumber 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_BASESNumber of bases in primary alignments that align to a UTR base for some gene, and not a coding base. -
INTRONIC_BASES
public long INTRONIC_BASESNumber 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_BASESNumber of bases in primary alignments that do not align to any gene. -
IGNORED_READS
public long IGNORED_READSNumber 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_READSNumber of aligned reads that are mapped to the correct strand. 0 if library is not strand-specific. -
INCORRECT_STRAND_READS
public long INCORRECT_STRAND_READSNumber 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_READSThe 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_READSThe 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_READSThe fraction of reads for which the transcription strand model could not be inferred. -
PCT_R1_TRANSCRIPT_STRAND_READS
public double PCT_R1_TRANSCRIPT_STRAND_READSThe 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_READSThe 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
Fraction of PF_ALIGNED_BASES that mapped to regions encoding ribosomal RNA, RIBOSOMAL_BASES/PF_ALIGNED_BASES -
PCT_CODING_BASES
public double PCT_CODING_BASESFraction of PF_ALIGNED_BASES that mapped to protein coding regions of genes, CODING_BASES/PF_ALIGNED_BASES -
PCT_UTR_BASES
public double PCT_UTR_BASESFraction of PF_ALIGNED_BASES that mapped to untranslated regions (UTR) of genes, UTR_BASES/PF_ALIGNED_BASES -
PCT_INTRONIC_BASES
public double PCT_INTRONIC_BASESFraction of PF_ALIGNED_BASES that correspond to gene introns, INTRONIC_BASES/PF_ALIGNED_BASES -
PCT_INTERGENIC_BASES
public double PCT_INTERGENIC_BASESFraction of PF_ALIGNED_BASES that mapped to intergenic regions of genomic DNA, INTERGENIC_BASES/PF_ALIGNED_BASES -
PCT_MRNA_BASES
public double PCT_MRNA_BASESSum 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_BASESThe 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_READSFraction 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_COVERAGEThe median coefficient of variation (CV) or stdev/mean for coverage values of the 1000 most highly expressed transcripts that have a length greater than the END_BIAS_BASES parameter. Ideal value = 0. -
MEDIAN_5PRIME_BIAS
public double MEDIAN_5PRIME_BIASThe median 5 prime bias of the 1000 most highly expressed transcripts that have a length greater than the END_BIAS_BASES parameter. The 5 prime bias is calculated per transcript as: mean coverage of the 5 prime-most number of bases divided by the mean coverage of the whole transcript. The number of end-bases used is specified by the END_BIAS_BASES parameter. -
MEDIAN_3PRIME_BIAS
public double MEDIAN_3PRIME_BIASThe median 3 prime bias of the 1000 most highly expressed transcripts that have a length greater than the END_BIAS_BASES parameter, where 3 prime bias is calculated per transcript as: mean coverage of the 3 prime-most number of bases, divided by the mean coverage of the whole transcript. The number of end-bases used is specified by the END_BIAS_BASES parameter. -
MEDIAN_5PRIME_TO_3PRIME_BIAS
public double MEDIAN_5PRIME_TO_3PRIME_BIASThe ratio of coverage at the 5 prime end to the 3 prime end based on the 1000 most highly expressed transcripts that have a length greater than the END_BIAS_BASES parameter. The number of end-bases used is specified by the END_BIAS_BASES parameter.
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Constructor Details
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RnaSeqMetrics
public RnaSeqMetrics()
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