File Info
- Filename
- NCI-H2228_FFPE_RNA_0001_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/NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_1_rna_metrics.txt
- Size
- 2.8 KB
- Workflow Run
- dev_rna_exp0008_1bb6229e
- Published
- Feb 26, 2026 11:46 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 NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT NCI-H2228_FFPE_RNA_0001_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 07:19:17 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 25454720569 25075416619 10588 22238922783 1681698346 1005909263 148875639 0 0 0 1827716 77808916 493872 0.022951 0.977049 0 0.886881 0.067066 0.040115 0.005937 0.953947 0.939732 0 0.489399 0.595601 0.78251 0.85878 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.267833 1 0.306292 2 0.359083 3 0.421099 4 0.48937 5 0.557915 6 0.623425 7 0.679334 8 0.737492 9 0.789434 10 0.84402 11 0.900115 12 0.951711 13 0.994288 14 1.024463 15 1.053335 16 1.082857 17 1.103894 18 1.116397 19 1.134888 20 1.15134 21 1.162047 22 1.17257 23 1.185121 24 1.189747 25 1.190584 26 1.19788 27 1.19986 28 1.202842 29 1.198289 30 1.190569 31 1.185441 32 1.176731 33 1.172926 34 1.165291 35 1.159609 36 1.155067 37 1.147115 38 1.140003 39 1.138176 40 1.135802 41 1.134567 42 1.13754 43 1.1454 44 1.147144 45 1.154548 46 1.147729 47 1.143501 48 1.137918 49 1.143917 50 1.150171 51 1.145118 52 1.139334 53 1.132543 54 1.139461 55 1.128104 56 1.120178 57 1.118544 58 1.117817 59 1.116406 60 1.108669 61 1.111222 62 1.117045 63 1.110721 64 1.102842 65 1.100756 66 1.098081 67 1.094557 68 1.087371 69 1.081205 70 1.073244 71 1.067573 72 1.065249 73 1.054914 74 1.05348 75 1.051856 76 1.046683 77 1.034307 78 1.032952 79 1.02637 80 1.011927 81 0.996541 82 0.987224 83 0.973386 84 0.959411 85 0.948302 86 0.93159 87 0.918535 88 0.899677 89 0.879113 90 0.855524 91 0.831997 92 0.807032 93 0.776695 94 0.743956 95 0.713719 96 0.683236 97 0.648136 98 0.613233 99 0.57733 100 0.53428