File Info

Filename
LungN_FFPE_L01_RNA_01_B23LG7FLT4_1_rna_metrics.txt
Full Path
s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0008_exp0011/B23LG7FLT4/nfcore_rnafusion__e7be3c7a--20260528-111100/QC/picard/LungN_FFPE_L01_RNA_01_B23LG7FLT4_1_rna_metrics.txt
Size
2.8 KB
Workflow Run
dev_rna_exp0008_exp0011-e7be3c7a_b
Published
May 28, 2026 5:17 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 LungN_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT LungN_FFPE_L01_RNA_01_B23LG7FLT4_1_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 May 28 21:25:48 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
66322799368	65216085290	27764	57286089385	5006649913	2517496981	405821247	0	0	0	20003542	219739550	1254935	0.083437	0.916563	0	0.878404	0.07677	0.038602	0.006223	0.955174	0.939236	0	0.673495	0.442057	0.620908	0.76102			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.265646
1	0.298886
2	0.352521
3	0.41618
4	0.48153
5	0.546652
6	0.613889
7	0.677035
8	0.745382
9	0.796523
10	0.844443
11	0.892404
12	0.934373
13	0.969903
14	0.998465
15	1.026575
16	1.042268
17	1.054724
18	1.074322
19	1.090933
20	1.095873
21	1.101274
22	1.119113
23	1.12976
24	1.137374
25	1.145904
26	1.147692
27	1.151866
28	1.161327
29	1.159856
30	1.157966
31	1.153058
32	1.142011
33	1.144171
34	1.140481
35	1.148855
36	1.150599
37	1.148869
38	1.140103
39	1.131415
40	1.127049
41	1.130566
42	1.140679
43	1.158977
44	1.173613
45	1.192033
46	1.200911
47	1.207769
48	1.20229
49	1.20237
50	1.193703
51	1.185894
52	1.182757
53	1.188278
54	1.185315
55	1.180123
56	1.172601
57	1.158082
58	1.157112
59	1.150558
60	1.146029
61	1.151201
62	1.154044
63	1.143545
64	1.141729
65	1.137272
66	1.126863
67	1.116401
68	1.113118
69	1.108471
70	1.096807
71	1.079549
72	1.073792
73	1.058771
74	1.051271
75	1.048652
76	1.046897
77	1.038036
78	1.032361
79	1.026721
80	1.01983
81	1.011756
82	1.003136
83	0.990268
84	0.974599
85	0.950979
86	0.925027
87	0.907133
88	0.889573
89	0.870214
90	0.840088
91	0.804455
92	0.776909
93	0.74897
94	0.724323
95	0.698814
96	0.668074
97	0.642246
98	0.605082
99	0.565324
100	0.524646