kiss2refgenome - fail in read kiss2refgenome using kissDE

Question

[cc86]

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"

[theobroma22]

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.

Answer 1

[leandro.ishi.lima]

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.

Answer 2

[cc86]

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!

[leandro.ishi.lima]

Dear cc86,

Could you describe the file you generated? The events.txt file output by kissplice2refgenome works fine when given to the software, but it does not fit your needs?

Thanks!

++