File Info
- Filename
- tih_rna_sample_00280_23H5VFLT4_s18_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_00280_23H5VFLT4_s18_rna_metrics.txt
- Size
- 2.8 KB
- Workflow Run
- dev_rna_exp0003_5f1fa79
- Published
- Mar 04, 2026 5:29 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_00280_23H5VFLT4_s18.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00280_23H5VFLT4_s18_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 00:27:34 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 26638215543 26140632965 9252 22692397261 1857825146 1424833253 165568053 0 0 0 1912649 77864014 312759 0.023975 0.976025 0 0.868089 0.07107 0.054506 0.006334 0.939159 0.921617 0 0.494909 0.618847 0.754673 0.93613 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.293466 1 0.341575 2 0.40686 3 0.481996 4 0.562276 5 0.633444 6 0.694704 7 0.751113 8 0.808527 9 0.859272 10 0.903447 11 0.945263 12 0.992476 13 1.031907 14 1.061105 15 1.082006 16 1.101868 17 1.125004 18 1.139743 19 1.153686 20 1.169899 21 1.17959 22 1.185425 23 1.190066 24 1.195906 25 1.192072 26 1.190565 27 1.193531 28 1.194105 29 1.189494 30 1.185469 31 1.184738 32 1.180058 33 1.177257 34 1.17925 35 1.184988 36 1.181974 37 1.170992 38 1.170087 39 1.165152 40 1.158081 41 1.15742 42 1.155631 43 1.161067 44 1.161863 45 1.162996 46 1.155836 47 1.14935 48 1.141188 49 1.139837 50 1.13198 51 1.126442 52 1.117742 53 1.114141 54 1.120159 55 1.123688 56 1.113524 57 1.104926 58 1.102707 59 1.091655 60 1.086259 61 1.086937 62 1.083035 63 1.082537 64 1.079244 65 1.080773 66 1.08446 67 1.073195 68 1.064693 69 1.058144 70 1.052885 71 1.044215 72 1.042457 73 1.031718 74 1.027269 75 1.020598 76 1.014683 77 1.001955 78 0.995964 79 0.991002 80 0.980657 81 0.963761 82 0.948768 83 0.933456 84 0.91825 85 0.907514 86 0.889381 87 0.873326 88 0.856215 89 0.837392 90 0.821304 91 0.803684 92 0.780236 93 0.752316 94 0.72553 95 0.696618 96 0.671001 97 0.645321 98 0.617125 99 0.589011 100 0.552311