Mercurial > repos > devteam > picard
view test-data/picard_CollectRnaSeqMetrics_test2.tab @ 28:c943f4a04af0 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 285fab1660daa944d6833ae1e059b30cb1e88309
| author | iuc |
|---|---|
| date | Mon, 25 Sep 2023 08:31:14 +0000 |
| parents | 2474cd44d10a |
| children |
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## htsjdk.samtools.metrics.StringHeader # picard.analysis.CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/opt/galaxy/galaxy/database/files/033/dataset_33778.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectRnaSeqMetrics_bam OUTPUT=/opt/galaxy/galaxy/database/files/033/dataset_33779.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 Jan 31 11:57:28 GMT 2019 ## 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 48870 48712 40205 8172 0 335 0 0 0 118 141 5 0.455598 0.544402 0.825361 0.167762 0 0.006877 0.993123 0.989912 0 0.801606 0.364744 0.224119 0.579618 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.228841 1 0.251223 2 0.223738 3 0.233838 4 0.256581 5 0.266966 6 0.271332 7 0.265645 8 0.260346 9 0.231289 10 0.269298 11 0.326408 12 0.373618 13 0.473463 14 0.54793 15 0.577498 16 0.542569 17 0.558467 18 0.650338 19 0.635229 20 0.574853 21 0.588563 22 0.650078 23 0.686162 24 0.634014 25 0.644335 26 0.631052 27 0.639668 28 0.705101 29 0.778048 30 0.736876 31 0.70567 32 0.707551 33 0.76318 34 0.852513 35 0.873038 36 0.943469 37 1.040668 38 1.070803 39 1.117516 40 1.166565 41 1.178104 42 1.151426 43 1.209844 44 1.198299 45 1.132792 46 1.149512 47 1.21306 48 1.345953 49 1.32854 50 1.309067 51 1.296104 52 1.346535 53 1.450902 54 1.475516 55 1.548883 56 1.628424 57 1.665228 58 1.612393 59 1.653451 60 1.599084 61 1.674705 62 1.670767 63 1.759351 64 1.771555 65 1.653379 66 1.634736 67 1.642939 68 1.587437 69 1.558905 70 1.571999 71 1.620224 72 1.57181 73 1.545141 74 1.433348 75 1.497304 76 1.693651 77 1.728257 78 1.754671 79 1.731652 80 1.713865 81 1.641332 82 1.515711 83 1.413569 84 1.441502 85 1.330984 86 1.269559 87 1.225153 88 1.133803 89 0.956795 90 0.793511 91 0.692324 92 0.542889 93 0.499087 94 0.422605 95 0.338219 96 0.272388 97 0.207126 98 0.152439 99 0.095696 100 0.069183