Mercurial > repos > devteam > picard
annotate test-data/picard_CollectRnaSeqMetrics_test1.tab @ 25:7d34178f2812 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit a0fcbda330469051d130fd0802c55960ae948e3b
| author | iuc |
|---|---|
| date | Tue, 11 Jun 2019 02:36:54 -0400 |
| parents | 5053a18d9bc8 |
| children | 3f254c5ced1d |
| rev | line source |
|---|---|
| 5 | 1 ## htsjdk.samtools.metrics.StringHeader |
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5053a18d9bc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents:
15
diff
changeset
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2 # CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/tmp/tmpYRm8q4/files/000/dataset_29.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectRnaSeqMetrics_bam OUTPUT=/tmp/tmpYRm8q4/files/000/dataset_30.dat ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false |
| 5 | 3 ## htsjdk.samtools.metrics.StringHeader |
|
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5053a18d9bc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents:
15
diff
changeset
|
4 # Started on: Sat Apr 14 09:29:39 CEST 2018 |
| 5 | 5 |
| 6 ## METRICS CLASS picard.analysis.RnaSeqMetrics | |
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19
5053a18d9bc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents:
15
diff
changeset
|
7 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 |
|
5053a18d9bc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents:
15
diff
changeset
|
8 48870 48712 0 38786 3735 6191 0 0 0 42 60 3 0.411765 0.588235 0 0.796231 0.076675 0.127094 0.796231 0.793657 0 0.867456 0.432948 0.262822 0.657143 |
| 5 | 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 |