Class 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 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.
      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.
    • Constructor Summary

      Constructors 
      Constructor Description
      RnaSeqMetrics()  
    • 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 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 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()