File Info
- Filename
- NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3_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_3_rna_metrics.txt
- Size
- 2.8 KB
- Workflow Run
- dev_rna_exp0008_1bb6229e
- Published
- Feb 26, 2026 11:27 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_3.Aligned.sortedByCoord.out.bam --OUTPUT NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3_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 07:12:38 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 24430025444 24051374680 13646 21350324253 1565388601 997744919 137903261 0 0 0 1058027 78329099 487211 0.013327 0.986673 0.000001 0.887697 0.065085 0.041484 0.005734 0.952782 0.938014 0 0.536281 0.557113 0.762787 0.835509 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.260937 1 0.300232 2 0.354446 3 0.414393 4 0.474515 5 0.540638 6 0.606394 7 0.666725 8 0.72583 9 0.776624 10 0.828617 11 0.88182 12 0.93329 13 0.971844 14 0.999547 15 1.027787 16 1.062572 17 1.086725 18 1.096844 19 1.11692 20 1.131997 21 1.142538 22 1.15188 23 1.165092 24 1.168891 25 1.166234 26 1.170959 27 1.180436 28 1.192934 29 1.188096 30 1.180351 31 1.174794 32 1.177316 33 1.17496 34 1.168953 35 1.162627 36 1.159712 37 1.151876 38 1.146859 39 1.14688 40 1.146308 41 1.14874 42 1.154589 43 1.16192 44 1.161452 45 1.165708 46 1.160535 47 1.156839 48 1.15047 49 1.162218 50 1.1701 51 1.171661 52 1.164981 53 1.156744 54 1.157864 55 1.143776 56 1.13933 57 1.137312 58 1.134276 59 1.13069 60 1.12585 61 1.13402 62 1.14068 63 1.133229 64 1.121423 65 1.11731 66 1.110215 67 1.09991 68 1.086745 69 1.079579 70 1.064413 71 1.058645 72 1.054661 73 1.045513 74 1.046048 75 1.041385 76 1.036566 77 1.028827 78 1.027564 79 1.024162 80 1.013248 81 0.998957 82 0.991052 83 0.978463 84 0.962916 85 0.951968 86 0.936369 87 0.922787 88 0.903614 89 0.885697 90 0.862892 91 0.837971 92 0.812022 93 0.782621 94 0.750417 95 0.717172 96 0.685054 97 0.652856 98 0.617023 99 0.579194 100 0.535779