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Filename
FFPE_HD834_01_RNA_0001_23LGNLLT4_2_rna_metrics.txt
Full Path
s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0005/A23LGNLLT4/nfcore_rnafusion__2cae617--20260515-145204/QC/picard/FFPE_HD834_01_RNA_0001_23LGNLLT4_2_rna_metrics.txt
Size
2.8 KB
Workflow Run
dev_rna_exp0005_2cae617
Published
May 16, 2026 6:19 AM

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## htsjdk.samtools.metrics.StringHeader
# CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT FFPE_HD834_01_RNA_0001_23LGNLLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_HD834_01_RNA_0001_23LGNLLT4_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: Sat May 16 10:14:44 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
78860246573	78015190491	33603	68796067599	5373619711	3374001348	471468230	0	0	0	7368116	234424275	1515306	0.030473	0.969527	0	0.881829	0.068879	0.043248	0.006043	0.950708	0.940521	0	0.488005	0.641866	0.766543	0.970731			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.302165
1	0.345694
2	0.402351
3	0.46927
4	0.54127
5	0.612683
6	0.679341
7	0.741945
8	0.7983
9	0.847302
10	0.897025
11	0.943574
12	0.986646
13	1.02539
14	1.052984
15	1.079772
16	1.10753
17	1.133026
18	1.141653
19	1.150194
20	1.158771
21	1.173522
22	1.178685
23	1.191876
24	1.202586
25	1.200168
26	1.197562
27	1.195257
28	1.194183
29	1.190775
30	1.186681
31	1.183485
32	1.179919
33	1.179307
34	1.175269
35	1.174898
36	1.168359
37	1.160628
38	1.154908
39	1.154552
40	1.157106
41	1.15654
42	1.150801
43	1.150477
44	1.149197
45	1.14924
46	1.146578
47	1.14537
48	1.145629
49	1.148066
50	1.146778
51	1.145981
52	1.141733
53	1.13692
54	1.139262
55	1.129501
56	1.119896
57	1.119527
58	1.110934
59	1.106652
60	1.099481
61	1.097544
62	1.100982
63	1.09363
64	1.091072
65	1.087159
66	1.086386
67	1.079899
68	1.071185
69	1.06236
70	1.04949
71	1.036053
72	1.034911
73	1.03242
74	1.024696
75	1.021669
76	1.012119
77	0.997877
78	0.992479
79	0.984727
80	0.970977
81	0.959059
82	0.947226
83	0.93516
84	0.916524
85	0.90698
86	0.893006
87	0.880772
88	0.865046
89	0.845706
90	0.825886
91	0.804663
92	0.779804
93	0.751886
94	0.726326
95	0.700991
96	0.674528
97	0.647058
98	0.615082
99	0.585
100	0.546598