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PCT_RIBOSOMAL_BASES is not 0 even though no ribosomal intervals are provided

Could someone help me to understand why
PCT_RIBOSOMAL_BASES is not 0 even though no ribosomal intervals are provided

Command line is
java -jar /opt/sam/Picard/1.117/CollectRnaSeqMetrics.jar REF_FLAT=~/Reference/mm10/mm10RefSeq INPUT=Aligned.sortedByCoord.out.bam OUTPUT=Aligned.sortedByCoord.out.picard STRAND_SPECIFICITY=NONE

The header reads
picard.analysis.CollectRnaSeqMetrics REF_FLAT=/home2/mchikina/mchikina/Reference/mm10/mm10RefSeq STRAND_SPECIFICITY=NONE INPUT=Aligned.sortedByCoord.out.bam OUTPUT=Aligned.sortedByCoord.out.picard MINIMUM_LENGTH=500 RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false

Issue · Github
by Sheila

Issue Number
268
State
closed
Last Updated
Milestone
Array
Closed By
vdauwera

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