File Info
- Filename
- tih_rna_sample_00088_23H5VFLT4_s02_rna_metrics.txt
- Full Path
- s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0003/B23H5VFLT4/nfcore_rnafusion_100M__5f1fa79--20260304-100305/QC/picard/tih_rna_sample_00088_23H5VFLT4_s02_rna_metrics.txt
- Size
- 2.8 KB
- Workflow Run
- dev_rna_exp0003_5f1fa79
- Published
- Mar 04, 2026 5:11 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 tih_rna_sample_00088_23H5VFLT4_s02.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00088_23H5VFLT4_s02_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: Thu Mar 05 00:07:54 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 25231314987 24863904683 18104 21588893979 1663703857 1421011943 190276800 0 0 0 6174798 74232101 272179 0.076794 0.923206 0.000001 0.868283 0.066912 0.057152 0.007653 0.935195 0.921577 0 0.550325 0.561819 0.708054 0.856823 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.339925 1 0.375292 2 0.428031 3 0.487592 4 0.545122 5 0.598838 6 0.658035 7 0.712645 8 0.779 9 0.844396 10 0.897032 11 0.943304 12 0.990872 13 1.032815 14 1.062444 15 1.079263 16 1.092942 17 1.113375 18 1.123339 19 1.13452 20 1.145189 21 1.157651 22 1.169527 23 1.186183 24 1.197017 25 1.202741 26 1.206028 27 1.2043 28 1.199737 29 1.194287 30 1.190538 31 1.189204 32 1.187486 33 1.186042 34 1.1866 35 1.197198 36 1.197663 37 1.193339 38 1.187321 39 1.175918 40 1.166556 41 1.158978 42 1.155791 43 1.15784 44 1.160059 45 1.160474 46 1.144194 47 1.13594 48 1.132778 49 1.132756 50 1.125914 51 1.119139 52 1.108007 53 1.101993 54 1.099958 55 1.094521 56 1.09125 57 1.081602 58 1.075252 59 1.064212 60 1.058722 61 1.05969 62 1.060447 63 1.05518 64 1.052284 65 1.049258 66 1.042303 67 1.039978 68 1.041601 69 1.044045 70 1.036454 71 1.028336 72 1.026047 73 1.024859 74 1.019892 75 1.015425 76 1.016023 77 1.014701 78 1.010521 79 1.010509 80 1.006032 81 0.99066 82 0.975747 83 0.958784 84 0.949165 85 0.934559 86 0.914233 87 0.89768 88 0.881134 89 0.864629 90 0.846813 91 0.833666 92 0.807585 93 0.779877 94 0.754442 95 0.728252 96 0.703825 97 0.679243 98 0.645616 99 0.61418 100 0.578818