Mercurial > repos > devteam > picard
view test-data/picard_CollectRnaSeqMetrics_test1.tab @ 14:465cbb0cf2eb draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f
| author | devteam |
|---|---|
| date | Wed, 07 Dec 2016 14:56:30 -0500 |
| parents | 3d4f1fa26f0e |
| children | 00fe2ff64467 |
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## htsjdk.samtools.metrics.StringHeader # 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 ## htsjdk.samtools.metrics.StringHeader # Started on: Mon Oct 06 22:24:48 EDT 2014 ## 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 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 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 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.31117 1 0.324521 2 0.280175 3 0.229683 4 0.247568 5 0.252404 6 0.37536 7 0.454337 8 0.498193 9 0.717955 10 0.852206 11 0.841585 12 0.883517 13 0.878327 14 0.971971 15 0.946456 16 1.096539 17 1.085217 18 1.030988 19 1.169726 20 1.06324 21 1.124029 22 1.021164 23 1.111695 24 1.036323 25 0.996034 26 1.08738 27 1.107549 28 0.955729 29 0.907313 30 1.049856 31 1.068308 32 1.05576 33 1.004803 34 1.044887 35 1.020916 36 0.914561 37 0.943721 38 0.938101 39 0.921157 40 1.059497 41 1.067667 42 1.164889 43 1.252036 44 1.294715 45 1.236472 46 1.169812 47 1.236597 48 1.067639 49 1.045102 50 0.994369 51 0.923449 52 0.915703 53 0.920667 54 0.840804 55 0.731542 56 0.785935 57 0.803421 58 0.797747 59 0.754627 60 0.748683 61 0.774967 62 0.880321 63 0.958948 64 1.066362 65 1.151358 66 1.289535 67 1.358181 68 1.33396 69 1.140164 70 1.260899 71 1.226678 72 1.259541 73 1.288495 74 1.484984 75 1.41511 76 1.351353 77 1.337399 78 1.340637 79 1.293356 80 1.327074 81 1.345788 82 1.469492 83 1.563011 84 1.528971 85 1.651207 86 1.640289 87 1.468521 88 1.482936 89 1.396498 90 1.326153 91 1.191411 92 1.054954 93 0.938397 94 0.82527 95 0.630468 96 0.417112 97 0.327528 98 0.308028 99 0.329076 100 0.315292