Mercurial > repos > devteam > picard
view test-data/picard_CollectRnaSeqMetrics_test3.tab @ 10:126c30841c38 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit f65b40f4eb3c3431b8d9213f86238deebfd6bc29
| author | devteam |
|---|---|
| date | Thu, 08 Dec 2016 06:43:24 -0500 |
| parents | |
| children | 486d7500da69 |
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## htsjdk.samtools.metrics.StringHeader # picard.analysis.CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/tmp/tmpRJquSu/files/000/dataset_14.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectRnaSeqMetrics_bam OUTPUT=/tmp/tmpRJquSu/files/000/dataset_15.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 ## htsjdk.samtools.metrics.StringHeader # Started on: Thu Dec 08 10:55:06 CET 2016 ## 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 0 9926 0 0 0 0 0.796231 0 0.203769 0.796231 0.793657 0 0.91593 0.430026 0.235755 1.402829 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.313906 1 0.333933 2 0.365536 3 0.344525 4 0.371353 5 0.378606 6 0.518015 7 0.51266 8 0.500497 9 0.690539 10 0.829611 11 0.784227 12 0.825037 13 0.730533 14 0.73133 15 0.693057 16 0.873759 17 0.774195 18 0.721989 19 0.791727 20 0.697702 21 0.698451 22 0.568885 23 0.689955 24 0.580475 25 0.602348 26 0.657286 27 0.600594 28 0.48185 29 0.478605 30 0.646053 31 0.689366 32 0.740073 33 0.695415 34 0.708419 35 0.714707 36 0.707421 37 0.793703 38 0.84384 39 0.819497 40 0.982412 41 1.172387 42 1.28116 43 1.379184 44 1.416285 45 1.32892 46 1.248258 47 1.308676 48 1.085518 49 1.006687 50 0.851309 51 0.693805 52 0.672921 53 0.684999 54 0.62579 55 0.529832 56 0.546564 57 0.566014 58 0.615824 59 0.565042 60 0.547677 61 0.642067 62 0.83636 63 0.937071 64 1.057465 65 1.168829 66 1.375228 67 1.489487 68 1.530099 69 1.287542 70 1.442585 71 1.347823 72 1.424913 73 1.468345 74 1.796846 75 1.79639 76 1.747908 77 1.76867 78 1.773528 79 1.670178 80 1.740083 81 1.809632 82 2.019967 83 2.201517 84 2.150455 85 2.327367 86 2.261259 87 1.929731 88 1.936627 89 1.80697 90 1.789004 91 1.642341 92 1.408203 93 1.159737 94 0.990047 95 0.697842 96 0.377809 97 0.243433 98 0.218816 99 0.223665 100 0.225079