error with calculateRPKM in customProDB
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javamng ▴ 10
@javamng-13627
Last seen 4.5 years ago

I am trying to create customProDB using the Human Ensembl 38.87 version.

Recently, when I run the claculateRPKM of the customProDB package after installing the related package, the same error is always output regardless of the data set.

By the way, I have seen the same error in the data that I have successfully executed before.

The error message is:

> RPKM <- calculateRPKM(bamFile, exon, proteincodingonly=TRUE, ids)
Error in keepSeqlevels(anno, seqlevels(galn)) :
  invalid seqlevels: KI270729.1, KI270743.1, GL000008.2, KI270747.1,
  KI270722.1, KI270742.1, KI270736.1, GL000224.1, KI270719.1, KI270712.1,
  KI270706.1, KI270725.1, KI270715.1, KI270749.1, KI270741.1, GL000221.1,
  KI270716.1, KI270751.1, KI270519.1, GL000214.1, KI270708.1, KI270730.1,
  KI270438.1, KI270737.1, KI270738.1, KI270748.1, KI270435.1, GL000208.1,
  KI270538.1, KI270756.1, KI270739.1, KI270757.1, KI270709.1, KI270746.1,
  KI270753.1, KI270589.1, KI270735.1, KI270745.1, KI270714.1, KI270732.1,
  KI270754.1, KI270710.1, KI270717.1, KI270724.1, KI270720.1, KI270723.1,
  KI270718.1, KI270317.1, KI270740.1, KI270755.1, KI270707.1, KI270579.1,
  KI270752.1, KI270512.1, KI270322.1, GL000226.1, KI270311.1, KI270366.1,
  KI270511.1, KI270448.1, KI270521.1, KI270581.1, KI270582.1, KI270515.1,
  KI270588.1, KI270591.1, KI270522.1, KI270507.1, KI270590.1, KI270584.1,
  KI270320.1, KI270382.1, KI270468.1, KI270467.1, KI270362.1, KI270517.1,
  KI270593.1, KI270528.1, KI270587.

 

>  sessionInfo()

R version 3.4.1 (2017-06-30)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
[1] customProDB_1.16.0   biomaRt_2.32.1       AnnotationDbi_1.38.2
[4] Biobase_2.36.2       IRanges_2.10.2       S4Vectors_0.14.3
[7] BiocGenerics_0.22.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.12               plyr_1.8.4
 [3] compiler_3.4.1             GenomeInfoDb_1.12.2
 [5] XVector_0.16.0             GenomicFeatures_1.28.4
 [7] bitops_1.0-6               tools_3.4.1
 [9] zlibbioc_1.22.0            digest_0.6.12
[11] bit_1.1-12                 AhoCorasickTrie_0.1.0
[13] RSQLite_2.0                memoise_1.1.0
[15] tibble_1.3.3               lattice_0.20-35
[17] BSgenome_1.44.0            rlang_0.1.1
[19] Matrix_1.2-10              DelayedArray_0.2.7
[21] DBI_0.7                    GenomeInfoDbData_0.99.0
[23] stringr_1.2.0              rtracklayer_1.36.4
[25] Biostrings_2.44.2          bit64_0.9-7
[27] grid_3.4.1                 XML_3.98-1.9
[29] BiocParallel_1.10.1        magrittr_1.5
[31] blob_1.1.0                 Rsamtools_1.28.0
[33] matrixStats_0.52.2         GenomicRanges_1.28.4
[35] GenomicAlignments_1.12.1   SummarizedExperiment_1.6.3
[37] stringi_1.1.5              RCurl_1.95-4.8
[39] VariantAnnotation_1.22.3

customProDB software error • 948 views
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I am getting the same error -- anyone find a fix?

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