|
9
|
1 ## htsjdk.samtools.metrics.StringHeader
|
|
|
2 # picard.analysis.CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_792.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=/Users/anton/galaxy-central/database/files/000/dataset_773.dat OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_793.dat REFERENCE_SEQUENCE=localref.fa ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
|
|
|
3 ## htsjdk.samtools.metrics.StringHeader
|
|
|
4 # Started on: Mon Oct 06 22:24:48 EDT 2014
|
|
|
5
|
|
|
6 ## METRICS CLASS picard.analysis.RnaSeqMetrics
|
|
|
7 PF_BASES PF_ALIGNED_BASES RIBOSOMAL_BASES CODING_BASES UTR_BASES INTRONIC_BASES INTERGENIC_BASES IGNORED_READS CORRECT_STRAND_READS INCORRECT_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
|
|
|
8 48870 48712 0 38786 3735 6191 0 0 0 0 0.796231 0.076675 0.127094 0.796231 0.793657 0 0.867456 0.432948 0.262822 0.657143
|
|
|
9
|
|
|
10 ## HISTOGRAM java.lang.Integer
|
|
|
11 normalized_position All_Reads.normalized_coverage
|
|
|
12 0 0.31117
|
|
|
13 1 0.324521
|
|
|
14 2 0.280175
|
|
|
15 3 0.229683
|
|
|
16 4 0.247568
|
|
|
17 5 0.252404
|
|
|
18 6 0.37536
|
|
|
19 7 0.454337
|
|
|
20 8 0.498193
|
|
|
21 9 0.717955
|
|
|
22 10 0.852206
|
|
|
23 11 0.841585
|
|
|
24 12 0.883517
|
|
|
25 13 0.878327
|
|
|
26 14 0.971971
|
|
|
27 15 0.946456
|
|
|
28 16 1.096539
|
|
|
29 17 1.085217
|
|
|
30 18 1.030988
|
|
|
31 19 1.169726
|
|
|
32 20 1.06324
|
|
|
33 21 1.124029
|
|
|
34 22 1.021164
|
|
|
35 23 1.111695
|
|
|
36 24 1.036323
|
|
|
37 25 0.996034
|
|
|
38 26 1.08738
|
|
|
39 27 1.107549
|
|
|
40 28 0.955729
|
|
|
41 29 0.907313
|
|
|
42 30 1.049856
|
|
|
43 31 1.068308
|
|
|
44 32 1.05576
|
|
|
45 33 1.004803
|
|
|
46 34 1.044887
|
|
|
47 35 1.020916
|
|
|
48 36 0.914561
|
|
|
49 37 0.943721
|
|
|
50 38 0.938101
|
|
|
51 39 0.921157
|
|
|
52 40 1.059497
|
|
|
53 41 1.067667
|
|
|
54 42 1.164889
|
|
|
55 43 1.252036
|
|
|
56 44 1.294715
|
|
|
57 45 1.236472
|
|
|
58 46 1.169812
|
|
|
59 47 1.236597
|
|
|
60 48 1.067639
|
|
|
61 49 1.045102
|
|
|
62 50 0.994369
|
|
|
63 51 0.923449
|
|
|
64 52 0.915703
|
|
|
65 53 0.920667
|
|
|
66 54 0.840804
|
|
|
67 55 0.731542
|
|
|
68 56 0.785935
|
|
|
69 57 0.803421
|
|
|
70 58 0.797747
|
|
|
71 59 0.754627
|
|
|
72 60 0.748683
|
|
|
73 61 0.774967
|
|
|
74 62 0.880321
|
|
|
75 63 0.958948
|
|
|
76 64 1.066362
|
|
|
77 65 1.151358
|
|
|
78 66 1.289535
|
|
|
79 67 1.358181
|
|
|
80 68 1.33396
|
|
|
81 69 1.140164
|
|
|
82 70 1.260899
|
|
|
83 71 1.226678
|
|
|
84 72 1.259541
|
|
|
85 73 1.288495
|
|
|
86 74 1.484984
|
|
|
87 75 1.41511
|
|
|
88 76 1.351353
|
|
|
89 77 1.337399
|
|
|
90 78 1.340637
|
|
|
91 79 1.293356
|
|
|
92 80 1.327074
|
|
|
93 81 1.345788
|
|
|
94 82 1.469492
|
|
|
95 83 1.563011
|
|
|
96 84 1.528971
|
|
|
97 85 1.651207
|
|
|
98 86 1.640289
|
|
|
99 87 1.468521
|
|
|
100 88 1.482936
|
|
|
101 89 1.396498
|
|
|
102 90 1.326153
|
|
|
103 91 1.191411
|
|
|
104 92 1.054954
|
|
|
105 93 0.938397
|
|
|
106 94 0.82527
|
|
|
107 95 0.630468
|
|
|
108 96 0.417112
|
|
|
109 97 0.327528
|
|
|
110 98 0.308028
|
|
|
111 99 0.329076
|
|
|
112 100 0.315292
|
|
|
113
|
