Hi all,
I am using ripSeek function from RIPSeeker package (on a RIP-seq data set), the following way:
seekOut <- ripSeek(bamPath=mybamfiles,
cNAME="EXP",
strandType="-",
biomart="ENSEMBL_MART_ENSEMBL",
biomaRt_dataset="hsapiens_gene_ensembl",
host="oct2016.archive.ensembl.org",
goAnno="org.Hs.eg.db",
annotateFormat="txt",
uniqueHit=T,
outDir="results",
exportFormat="BED",
multicore=T
)
It stops with an error, the last lines of the output being:
*** 1 do not have any alignment.
*** 2 do not have any alignment.
*** 3 do not have any alignment.
*** 4 do not have any alignment.
*** 5 do not have any alignment.
*** 6 do not have any alignment.
*** 7 do not have any alignment.
*** 8 do not have any alignment.
*** 9 do not have any alignment.
*** 10 do not have any alignment.
*** 11 do not have any alignment.
*** 12 do not have any alignment.
*** 13 do not have any alignment.
*** 14 do not have any alignment.
*** 15 do not have any alignment.
*** 16 do not have any alignment.
*** 17 do not have any alignment.
*** 18 do not have any alignment.
*** 19 do not have any alignment.
*** 20 do not have any alignment.
*** 21 do not have any alignment.
*** 22 do not have any alignment.
*** X do not have any alignment.
*** Y do not have any alignment.
*** MT do not have any alignment.
Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :
subscript contains NAs or out-of-bounds indices
I have checked different threads and can get rid off the "NSBS.." error when I set strandType to NULL.
But I guess it is a bug? Should I be confident about my results without the strand information?
Also I still get the "... do not have any alignement" output, while the reads I input align to those chromosomes.
Does anyone know what is happening there?
Thanks!
sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Scientific Linux release 6.5 (Carbon)
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] grid stats4 parallel stats graphics grDevices utils
[8] datasets methods base
other attached packages:
[1] GO.db_3.2.2 org.Hs.eg.db_3.2.3
[3] AnnotationDbi_1.32.3 biomaRt_2.26.1
[5] ChIPpeakAnno_3.4.6 RSQLite_1.1-2
[7] VennDiagram_1.6.17 futile.logger_1.4.3
[9] RIPSeeker_1.10.0 rtracklayer_1.30.4
[11] GenomicAlignments_1.6.3 Rsamtools_1.22.0
[13] Biostrings_2.38.4 XVector_0.10.0
[15] SummarizedExperiment_1.0.2 Biobase_2.30.0
[17] GenomicRanges_1.22.4 GenomeInfoDb_1.6.3
[19] IRanges_2.4.8 S4Vectors_0.8.11
[21] BiocGenerics_0.16.1 limma_3.26.9
loaded via a namespace (and not attached):
[1] Rcpp_0.12.8 AnnotationHub_2.2.5
[3] BiocInstaller_1.20.3 regioneR_1.2.3
[5] GenomicFeatures_1.22.13 bitops_1.0-6
[7] futile.options_1.0.0 tools_3.3.0
[9] zlibbioc_1.16.0 digest_0.6.11
[11] memoise_1.0.0 lattice_0.20-33
[13] BSgenome_1.38.0 Matrix_1.2-6
[15] graph_1.48.0 shiny_1.0.0
[17] DBI_0.5-1 httr_1.2.1
[19] multtest_2.26.0 R6_2.2.0
[21] XML_3.98-1.5 survival_2.40-1
[23] RBGL_1.46.0 BiocParallel_1.4.3
[25] ensembldb_1.2.2 lambda.r_1.1.9
[27] matrixStats_0.51.0 htmltools_0.3.5
[29] splines_3.3.0 MASS_7.3-45
[31] xtable_1.8-2 mime_0.5
[33] interactiveDisplayBase_1.8.0 httpuv_1.3.3
[35] RCurl_1.95-4.8
I am using ripSeek function from RIPSeeker package (on a RIP-seq data set), the following way:
seekOut <- ripSeek(bamPath=mybamfiles,
cNAME="EXP",
strandType="-",
biomart="ENSEMBL_MART_ENSEMBL",
biomaRt_dataset="hsapiens_gene_ensembl",
host="oct2016.archive.ensembl.org",
goAnno="org.Hs.eg.db",
annotateFormat="txt",
uniqueHit=T,
outDir="results",
exportFormat="BED",
multicore=T
)
It stops with an error, the last lines of the output being:
*** 1 do not have any alignment.
*** 2 do not have any alignment.
*** 3 do not have any alignment.
*** 4 do not have any alignment.
*** 5 do not have any alignment.
*** 6 do not have any alignment.
*** 7 do not have any alignment.
*** 8 do not have any alignment.
*** 9 do not have any alignment.
*** 10 do not have any alignment.
*** 11 do not have any alignment.
*** 12 do not have any alignment.
*** 13 do not have any alignment.
*** 14 do not have any alignment.
*** 15 do not have any alignment.
*** 16 do not have any alignment.
*** 17 do not have any alignment.
*** 18 do not have any alignment.
*** 19 do not have any alignment.
*** 20 do not have any alignment.
*** 21 do not have any alignment.
*** 22 do not have any alignment.
*** X do not have any alignment.
*** Y do not have any alignment.
*** MT do not have any alignment.
Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :
subscript contains NAs or out-of-bounds indices
I have checked different threads and can get rid off the "NSBS.." error when I set strandType to NULL.
But I guess it is a bug? Should I be confident about my results without the strand information?
Also I still get the "... do not have any alignement" output, while the reads I input align to those chromosomes.
Does anyone know what is happening there?
Thanks!
sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Scientific Linux release 6.5 (Carbon)
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] grid stats4 parallel stats graphics grDevices utils
[8] datasets methods base
other attached packages:
[1] GO.db_3.2.2 org.Hs.eg.db_3.2.3
[3] AnnotationDbi_1.32.3 biomaRt_2.26.1
[5] ChIPpeakAnno_3.4.6 RSQLite_1.1-2
[7] VennDiagram_1.6.17 futile.logger_1.4.3
[9] RIPSeeker_1.10.0 rtracklayer_1.30.4
[11] GenomicAlignments_1.6.3 Rsamtools_1.22.0
[13] Biostrings_2.38.4 XVector_0.10.0
[15] SummarizedExperiment_1.0.2 Biobase_2.30.0
[17] GenomicRanges_1.22.4 GenomeInfoDb_1.6.3
[19] IRanges_2.4.8 S4Vectors_0.8.11
[21] BiocGenerics_0.16.1 limma_3.26.9
loaded via a namespace (and not attached):
[1] Rcpp_0.12.8 AnnotationHub_2.2.5
[3] BiocInstaller_1.20.3 regioneR_1.2.3
[5] GenomicFeatures_1.22.13 bitops_1.0-6
[7] futile.options_1.0.0 tools_3.3.0
[9] zlibbioc_1.16.0 digest_0.6.11
[11] memoise_1.0.0 lattice_0.20-33
[13] BSgenome_1.38.0 Matrix_1.2-6
[15] graph_1.48.0 shiny_1.0.0
[17] DBI_0.5-1 httr_1.2.1
[19] multtest_2.26.0 R6_2.2.0
[21] XML_3.98-1.5 survival_2.40-1
[23] RBGL_1.46.0 BiocParallel_1.4.3
[25] ensembldb_1.2.2 lambda.r_1.1.9
[27] matrixStats_0.51.0 htmltools_0.3.5
[29] splines_3.3.0 MASS_7.3-45
[31] xtable_1.8-2 mime_0.5
[33] interactiveDisplayBase_1.8.0 httpuv_1.3.3
[35] RCurl_1.95-4.8