Question: kiss2refgenome - fail in read kiss2refgenome using kissDE
0
gravatar for cc86
14 days ago by
cc860
cc860 wrote:

HI!

I am trying to run the last step (kissDE) of the kiss2refgenome pipeline (http://kissplice.prabi.fr/sknsh/ ) , but I can't load the kiss2refgenome output files using the counts option:

kissplice2counts('results_test.k2g', counts = 1, pairedEnd = F, k2rg = TRUE) Error in matrix(0, nrow = length(lBcc)) : data is too long

Do you why this is happening ?

Thanks In advance ! cc


STAR_2.5.2b
kissplice-2.4.0-p1
kissplice2refgenome-1.0.0

R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Sierra 10.12.3

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] kissDE_1.4.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.9                locfit_1.5-9.1
 [3] lattice_0.20-34            gtools_3.5.0
 [5] foreach_1.4.3              glmnet_2.0-5
 [7] assertthat_0.1             digest_0.6.12
 [9] GenomeInfoDb_1.10.3        plyr_1.8.4
[11] backports_1.0.5            acepack_1.4.1
[13] stats4_3.3.2               RSQLite_1.1-2
[15] ggplot2_2.2.1              zlibbioc_1.20.0
[17] lazyeval_0.2.0             data.table_1.10.4
[19] annotate_1.52.1            S4Vectors_0.12.1
[21] R.utils_2.5.0              R.oo_1.21.0
[23] rpart_4.1-10               Matrix_1.2-8
[25] checkmate_1.8.2            splines_3.3.2
[27] BiocParallel_1.8.1         geneplotter_1.52.0
[29] stringr_1.2.0              foreign_0.8-67
[31] htmlwidgets_0.8            RCurl_1.95-4.8
[33] munsell_0.4.3              bsseq_1.10.0
[35] BiocGenerics_0.20.0        base64enc_0.1-3
[37] htmltools_0.3.5            nnet_7.3-12
[39] SummarizedExperiment_1.4.0 tibble_1.2
[41] gridExtra_2.2.1            htmlTable_1.9
[43] codetools_0.2-15           Hmisc_4.0-2
[45] IRanges_2.8.1              matrixStats_0.51.0
[47] XML_3.98-1.5               permute_0.9-4
[49] bitops_1.0-6               R.methodsS3_1.7.1
[51] grid_3.3.2                 xtable_1.8-2
[53] gtable_0.2.0               DBI_0.5-1
[55] magrittr_1.5               scales_0.4.1
[57] stringi_1.1.2              XVector_0.14.0
[59] genefilter_1.56.0          limma_3.30.12
[61] latticeExtra_0.6-28        DSS_2.14.0
[63] aod_1.3                    Formula_1.2-1
[65] RColorBrewer_1.1-2         iterators_1.0.8
[67] tools_3.3.2                Biobase_2.34.0
[69] DESeq2_1.14.1              parallel_3.3.2
[71] survival_2.40-1            AnnotationDbi_1.36.2
[73] colorspace_1.3-2           cluster_2.0.5
[75] GenomicRanges_1.26.3       memoise_1.0.0
[77] knitr_1.15.1"
kissplice • 97 views
ADD COMMENTlink modified 9 days ago • written 14 days ago by cc860

I would think that one of your previous steps ran but with errors, and so the output didn't complete. Did you open and view the .k2g file to see what it looks like? According to the error the file is not complete, formatted properly. First, I would write out FALSE like you did for TRUE, and run it again if you can't view the file in a word editor or other. I've found that if my ubuntu is acting unstable I can't use the T/F abbreviation in my R code and get an error when I try to load a file.

ADD REPLYlink written 13 days ago by theobroma22390
0
gravatar for leandro.ishi.lima
9 days ago by
leandro.ishi.lima20 wrote:

Dear cc86,

The page http://kissplice.prabi.fr/sknsh/ is outdated (our fault). The updated page for the pipeline you are looking for can be found here: http://kissplice.prabi.fr/pipeline_ks_farline/ . Thanks for the report, we will do a redirecting of http://kissplice.prabi.fr/sknsh/ to http://kissplice.prabi.fr/pipeline_ks_farline/ from now on. Could you try then the pipeline described at http://kissplice.prabi.fr/pipeline_ks_farline/ and post then the results?

Thank you very much.

ADD COMMENTlink written 9 days ago by leandro.ishi.lima20
0
gravatar for cc86
9 days ago by
cc860
cc860 wrote:

Dear Leandro,

I tried using the pipeline described in the URL, but I still get the same message. Could it be because the version of the software? If I use the events.txt file, instead of the one that I generated, the software works fine.

> myCounts <- kissplice2counts('test.txt', counts = 2, pairedEnd = FALSE, exonicReads = FALSE, k2rg = TRUE)
Error in matrix(0, nrow = length(lBcc)) : data is too long

Thanks!

ADD COMMENTlink written 9 days ago by cc860
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 694 users visited in the last hour