Produces RNA alignment metrics for a SAM or BAM file.
java -jar picard.jar CollectRnaSeqMetrics I=input.bam O=output.RNA_Metrics REF_FLAT=ref_flat.txt STRAND=SECOND_READ_TRANSCRIPTION_STRAND RIBOSOMAL_INTERVALS=ribosomal.interval_list
REF_FLAT (File) Gene annotations in refFlat form. Format described here: http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html#RefFlat Required.
RIBOSOMAL_INTERVALS (File) Location of rRNA sequences in genome, in interval_list format. If not specified no bases will be identified as being ribosomal. Format described here: Default value: null.
STRAND_SPECIFICITY (StrandSpecificity) For strand-specific library prep. For unpaired reads, use FIRST_READ_TRANSCRIPTION_STRAND if the reads are expected to be on the transcription strand. Required. Possible values: {NONE, FIRST_READ_TRANSCRIPTION_STRAND, SECOND_READ_TRANSCRIPTION_STRAND}
MINIMUM_LENGTH (Integer) When calculating coverage based values (e.g. CV of coverage) only use transcripts of this length or greater. Default value: 500. This option can be set to 'null' to clear the default value.
CHART_OUTPUT (File) The PDF file to write out a plot of normalized position vs. coverage. Default value: null.
IGNORE_SEQUENCE (String) If a read maps to a sequence specified with this option, all the bases in the read are counted as ignored bases. These reads are not counted as Default value: null. This option may be specified 0 or more times.
RRNA_FRAGMENT_PERCENTAGE (Double) This percentage of the length of a fragment must overlap one of the ribosomal intervals for a read or read pair to be considered rRNA. Default value: 0.8. This option can be set to 'null' to clear the default value.
METRIC_ACCUMULATION_LEVEL (MetricAccumulationLevel) The level(s) at which to accumulate metrics. Default value: [ALL_READS]. This option can be set to 'null' to clear the default value. Possible values: {ALL_READS, SAMPLE, LIBRARY, READ_GROUP} This option may be specified 0 or more times. This option can be set to 'null' to clear the default list.
INPUT (File) Input SAM or BAM file. Required.
OUTPUT (File) File to write the output to. Required.
ASSUME_SORTED (Boolean) If true (default), then the sort order in the header file will be ignored. Default value: true. This option can be set to 'null' to clear the default value. Possible values: {true, false}
STOP_AFTER (Long) Stop after processing N reads, mainly for debugging. Default value: 0. This option can be set to 'null' to clear the default value.