File Info

Filename
SkinN_FFPE_L07_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/SkinN_FFPE_L07_RNA_01_B23LG7FLT4_1_rna_metrics.txt
Size
2.9 KB
Workflow Run
dev_rna_exp0008_exp0011-e7be3c7a_b
Published
May 28, 2026 5:11 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 SkinN_FFPE_L07_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT SkinN_FFPE_L07_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 22:48:56 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
45942870724	45032739903	65756	39259998575	3168395303	2185848909	418431360	0	0	0	9246847	160123555	850599	0.054595	0.945405	0.000001	0.87181	0.070358	0.048539	0.009292	0.942168	0.923503	0	0.784539	0.336661	0.548617	0.720445			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.299251
1	0.338456
2	0.397601
3	0.458332
4	0.511158
5	0.563309
6	0.611553
7	0.655712
8	0.701289
9	0.741215
10	0.767568
11	0.803865
12	0.841898
13	0.87585
14	0.915559
15	0.936173
16	0.958307
17	0.968926
18	0.974166
19	0.990889
20	1.005884
21	1.016801
22	1.024855
23	1.029005
24	1.040283
25	1.053941
26	1.061615
27	1.072392
28	1.086418
29	1.081394
30	1.087505
31	1.099134
32	1.112859
33	1.129489
34	1.121165
35	1.124769
36	1.130801
37	1.129913
38	1.145913
39	1.150585
40	1.16111
41	1.174704
42	1.183578
43	1.183431
44	1.187833
45	1.184326
46	1.167794
47	1.163746
48	1.15936
49	1.160874
50	1.160699
51	1.150252
52	1.149261
53	1.160083
54	1.171608
55	1.173309
56	1.176128
57	1.165467
58	1.157859
59	1.155744
60	1.169265
61	1.178428
62	1.180886
63	1.16208
64	1.15926
65	1.156085
66	1.152254
67	1.146562
68	1.152176
69	1.148859
70	1.141223
71	1.127678
72	1.123457
73	1.126258
74	1.127459
75	1.129522
76	1.137386
77	1.131031
78	1.116913
79	1.100602
80	1.080182
81	1.066008
82	1.048028
83	1.045951
84	1.042347
85	1.029018
86	1.012937
87	1.002399
88	0.985796
89	0.960728
90	0.925513
91	0.884165
92	0.842065
93	0.787953
94	0.755918
95	0.729478
96	0.686717
97	0.655973
98	0.611851
99	0.561876
100	0.51555