File Info
- Filename
- FFPE_HD789_01_RNA_0002_B23LG7FLT4_1_rna_metrics.txt
- Full Path
- s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0008/B23LG7FLT4/nfcore_rnafusion_100M__1bb6229e--20260226-142939/QC/picard/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1_rna_metrics.txt
- Size
- 2.9 KB
- Workflow Run
- dev_rna_exp0008_1bb6229e
- Published
- Feb 26, 2026 11:14 PM
Content
View in new tab## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_HD789_01_RNA_0002_B23LG7FLT4_1_rna_metrics.txt --TMP_DIR ./tmp --MINIMUM_LENGTH 500 --RRNA_FRAGMENT_PERCENTAGE 0.8 --METRIC_ACCUMULATION_LEVEL ALL_READS --END_BIAS_BASES 100 --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 --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false ## htsjdk.samtools.metrics.StringHeader # Started on: Fri Feb 27 07:05:30 GMT 2026 ## METRICS CLASS picard.analysis.RnaSeqMetrics PF_BASES PF_ALIGNED_BASES RIBOSOMAL_BASES CODING_BASES UTR_BASES INTRONIC_BASES INTERGENIC_BASES IGNORED_READS CORRECT_STRAND_READS INCORRECT_STRAND_READS NUM_R1_TRANSCRIPT_STRAND_READS NUM_R2_TRANSCRIPT_STRAND_READS NUM_UNEXPLAINED_READS PCT_R1_TRANSCRIPT_STRAND_READS PCT_R2_TRANSCRIPT_STRAND_READS PCT_RIBOSOMAL_BASES PCT_CODING_BASES PCT_UTR_BASES PCT_INTRONIC_BASES PCT_INTERGENIC_BASES PCT_MRNA_BASES PCT_USABLE_BASES PCT_CORRECT_STRAND_READS MEDIAN_CV_COVERAGE MEDIAN_5PRIME_BIAS MEDIAN_3PRIME_BIAS MEDIAN_5PRIME_TO_3PRIME_BIAS SAMPLE LIBRARY READ_GROUP 25853407413 25508346039 26162 22473579112 1798561291 1082377591 153801883 0 0 0 1734477 78070467 577417 0.021734 0.978266 0.000001 0.881028 0.070509 0.042432 0.006029 0.951537 0.938837 0 0.508789 0.637943 0.731004 0.967337 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.305984 1 0.347628 2 0.403727 3 0.468639 4 0.542695 5 0.611823 6 0.674736 7 0.738412 8 0.801128 9 0.852974 10 0.896348 11 0.947506 12 0.996193 13 1.032602 14 1.062754 15 1.089614 16 1.116431 17 1.135684 18 1.145864 19 1.157811 20 1.179967 21 1.199578 22 1.207842 23 1.213678 24 1.214484 25 1.212977 26 1.211991 27 1.212448 28 1.210042 29 1.200532 30 1.192166 31 1.188065 32 1.180616 33 1.173996 34 1.168968 35 1.173096 36 1.168391 37 1.161263 38 1.153433 39 1.149578 40 1.151434 41 1.150233 42 1.144557 43 1.143095 44 1.141395 45 1.140782 46 1.130932 47 1.127151 48 1.126035 49 1.128367 50 1.1281 51 1.126211 52 1.122059 53 1.124494 54 1.131171 55 1.129786 56 1.124728 57 1.126456 58 1.120837 59 1.109781 60 1.108009 61 1.103541 62 1.102216 63 1.097447 64 1.090582 65 1.087186 66 1.094607 67 1.087059 68 1.080706 69 1.074599 70 1.067688 71 1.058765 72 1.055592 73 1.046293 74 1.035504 75 1.026557 76 1.014424 77 0.997451 78 0.993974 79 0.985415 80 0.970797 81 0.951941 82 0.940942 83 0.92395 84 0.906077 85 0.894455 86 0.878882 87 0.863383 88 0.846746 89 0.829281 90 0.814632 91 0.794155 92 0.769495 93 0.745692 94 0.716336 95 0.687931 96 0.662964 97 0.635259 98 0.6025 99 0.574183 100 0.538166