File Info
- Filename
- NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_2_rna_metrics.txt
- Full Path
- s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0008/B23LG7FLT4/nfcore_rnafusion_100M__5f1fa793--20260303-130000/QC/picard/NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_2_rna_metrics.txt
- Size
- 2.8 KB
- Workflow Run
- dev_rna_exp0008_5f1fa793
- Published
- Mar 03, 2026 7:01 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_2.Aligned.sortedByCoord.out.bam --OUTPUT NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_2_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: Wed Mar 04 01:42:50 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 25085787072 24708945284 14324 21954345762 1639084196 971276765 144224237 0 0 0 1364578 78318574 485867 0.017125 0.982875 0.000001 0.888518 0.066336 0.039309 0.005837 0.954854 0.94051 0 0.499355 0.585205 0.794811 0.8265 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.264641 1 0.301971 2 0.353186 3 0.415262 4 0.484237 5 0.553155 6 0.620961 7 0.680046 8 0.739346 9 0.791456 10 0.843692 11 0.898097 12 0.94957 13 0.990335 14 1.019381 15 1.045199 16 1.079669 17 1.102452 18 1.114186 19 1.131296 20 1.146402 21 1.158113 22 1.167048 23 1.179856 24 1.185099 25 1.187012 26 1.195728 27 1.198866 28 1.202401 29 1.197607 30 1.189337 31 1.182136 32 1.174842 33 1.168168 34 1.159032 35 1.152605 36 1.14881 37 1.140887 38 1.133342 39 1.131154 40 1.12981 41 1.128556 42 1.131439 43 1.140702 44 1.141032 45 1.148948 46 1.143544 47 1.141647 48 1.138112 49 1.145212 50 1.150292 51 1.145969 52 1.138391 53 1.129839 54 1.136064 55 1.124973 56 1.117988 57 1.117192 58 1.115958 59 1.113205 60 1.107488 61 1.10915 62 1.115506 63 1.11 64 1.101794 65 1.09861 66 1.095582 67 1.091779 68 1.083717 69 1.075027 70 1.067129 71 1.063702 72 1.059473 73 1.050233 74 1.052634 75 1.054986 76 1.052088 77 1.039981 78 1.03906 79 1.033221 80 1.018721 81 1.005079 82 0.99785 83 0.984534 84 0.971472 85 0.960768 86 0.944622 87 0.930277 88 0.911729 89 0.890626 90 0.86812 91 0.844687 92 0.819301 93 0.788746 94 0.754405 95 0.721939 96 0.690811 97 0.655638 98 0.620055 99 0.584657 100 0.543971