File Info
- Filename
- SK-BR-3_FFPE_01_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/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_1_rna_metrics.txt
- Size
- 2.8 KB
- Workflow Run
- dev_rna_exp0008_1bb6229e
- Published
- Feb 26, 2026 11:20 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 SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT SK-BR-3_FFPE_01_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 06:41:51 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 25115273799 24758075188 24230 21899158569 1660495276 1034994510 163402603 0 0 0 3324881 77931950 518949 0.040918 0.959082 0.000001 0.884526 0.067069 0.041804 0.0066 0.951595 0.938061 0 0.518404 0.594137 0.744374 0.915734 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.280236 1 0.325607 2 0.38655 3 0.452339 4 0.52296 5 0.591002 6 0.658352 7 0.72643 8 0.787167 9 0.839605 10 0.888329 11 0.938841 12 0.98818 13 1.02787 14 1.062959 15 1.093124 16 1.12163 17 1.144264 18 1.158669 19 1.168441 20 1.176213 21 1.193979 22 1.204789 23 1.211635 24 1.215535 25 1.212501 26 1.218426 27 1.215966 28 1.215099 29 1.205835 30 1.203389 31 1.202891 32 1.203872 33 1.205404 34 1.19414 35 1.190916 36 1.186707 37 1.176444 38 1.169589 39 1.159037 40 1.155317 41 1.148576 42 1.146446 43 1.160098 44 1.15762 45 1.158859 46 1.157614 47 1.153126 48 1.152568 49 1.157762 50 1.14562 51 1.145792 52 1.143655 53 1.135586 54 1.136737 55 1.133326 56 1.124506 57 1.113889 58 1.108263 59 1.101447 60 1.098177 61 1.096804 62 1.100151 63 1.095737 64 1.087991 65 1.085485 66 1.092877 67 1.086587 68 1.083982 69 1.075193 70 1.065174 71 1.053185 72 1.05088 73 1.045235 74 1.033277 75 1.016423 76 1.000648 77 0.98672 78 0.98143 79 0.969667 80 0.957867 81 0.939104 82 0.921274 83 0.907332 84 0.887805 85 0.874504 86 0.858376 87 0.845045 88 0.829146 89 0.813379 90 0.793618 91 0.778699 92 0.763645 93 0.739405 94 0.716643 95 0.693684 96 0.67318 97 0.650551 98 0.62385 99 0.591204 100 0.552112