File Info
- Filename
- SK-BR-3_FFPE_01_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__5f1fa793--20260303-130000/QC/picard/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_3_rna_metrics.txt
- Size
- 2.9 KB
- Workflow Run
- dev_rna_exp0008_5f1fa793
- Published
- Mar 03, 2026 7:16 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_3.Aligned.sortedByCoord.out.bam --OUTPUT SK-BR-3_FFPE_01_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: Wed Mar 04 01:59:29 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 25616288791 25274024461 18491 22392466058 1677550540 1048966034 155023338 0 0 0 2365293 79035158 496185 0.029057 0.970943 0.000001 0.885987 0.066374 0.041504 0.006134 0.952362 0.939637 0 0.516028 0.57993 0.748904 0.854278 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.273445 1 0.314997 2 0.373444 3 0.440561 4 0.50938 5 0.577713 6 0.645904 7 0.714011 8 0.77312 9 0.824584 10 0.875707 11 0.926221 12 0.971445 13 1.010264 14 1.046362 15 1.079681 16 1.113266 17 1.137575 18 1.153824 19 1.164666 20 1.172043 21 1.192127 22 1.203139 23 1.209644 24 1.214591 25 1.213434 26 1.218429 27 1.219554 28 1.218768 29 1.212288 30 1.208402 31 1.203788 32 1.201011 33 1.20258 34 1.192321 35 1.191238 36 1.187631 37 1.178884 38 1.173916 39 1.164886 40 1.164794 41 1.160123 42 1.158575 43 1.170877 44 1.169754 45 1.170137 46 1.164833 47 1.160486 48 1.161787 49 1.166401 50 1.154784 51 1.155989 52 1.153496 53 1.14553 54 1.146147 55 1.142819 56 1.135673 57 1.128011 58 1.120052 59 1.112473 60 1.107292 61 1.106093 62 1.107879 63 1.102878 64 1.092647 65 1.089601 66 1.086356 67 1.07577 68 1.070016 69 1.064282 70 1.055059 71 1.043425 72 1.04202 73 1.03556 74 1.026965 75 1.014054 76 0.997904 77 0.985366 78 0.97935 79 0.970397 80 0.96018 81 0.94212 82 0.925512 83 0.9113 84 0.892803 85 0.879579 86 0.86305 87 0.851541 88 0.835986 89 0.819174 90 0.799449 91 0.783461 92 0.765852 93 0.742491 94 0.718518 95 0.694817 96 0.67426 97 0.649478 98 0.621776 99 0.590604 100 0.552828