I am trying to use the ChIPQC package with ChIP-Seq data and I am getting an empty cross-correlation plot. I am using bwa mem to do the alignment, after which I remove multi-mappers and supplementary alignments. I then run ChIPQCsample (setting runCrossCorr to TRUE) for one of my samples and I get a bunch of warnings about integer overflow. This is the sample object output (using one chromosome):
ChIPQCsample
Number of Mapped reads: 4433141
Number of Mapped reads passing MapQ filter: 4295636
Percentage Of Reads as Non-Duplicates (NRF): 100(0)
Percentage Of Reads in Blacklisted Regions: NA
SSD: 21.2717230413828
Fragment Length Cross-Coverage:
Relative Cross-Coverage:
Percentage Of Reads in GenomicFeature:
ProportionOfCounts
5utrs NA
3UTRs NA
CountsinReads NA
Introns NA
Transcripts NA
Promoters500 NA
Promoters2000to500 NA
LongPromoter20000to2000 NA
Percentage Of Reads in Peaks: NA
Number of Peaks: 0
GRanges object with 0 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
-------
seqinfo: no sequences
Then, when I run ChIPQCreport, it produces a coverage histogram plot and a cross coverage plot, after which it errors out with this error:
Error in names(res) <- c("Reads", "Map%", "Filt%", "Dup%", "ReadL", "FragL", :
'names' attribute [9] must be the same length as the vector [7]
In addition: Warning message:
Removed 300 rows containing missing values (geom_path).
I've found posts where other people had this error and it was due to having single-end reads, but I'm not using single-end reads. Here are the plots:
Coverage Histogram:
Cross Correlation:
As you can see, the cross correlation plot is empty. I have been able to create a cross correlation plot using other software, so I'm not sure why this is not working. Any help would be highly appreciated.
- Nik.
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.4 LTS
Matrix products: default
BLAS: /afs/genomecenter.ucdavis.edu/software/R/3.6.1/lssc0-linux/lib/R/lib/libRblas.so
LAPACK: /afs/genomecenter.ucdavis.edu/software/R/3.6.1/lssc0-linux/lib/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US LC_NUMERIC=C LC_TIME=en_US
[4] LC_COLLATE=en_US LC_MONETARY=en_US LC_MESSAGES=en_US
[7] LC_PAPER=en_US LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] ChIPQC_1.20.0 DiffBind_2.12.0
[3] SummarizedExperiment_1.14.1 DelayedArray_0.10.0
[5] BiocParallel_1.18.1 matrixStats_0.55.0
[7] Biobase_2.44.0 GenomicRanges_1.36.1
[9] GenomeInfoDb_1.20.0 IRanges_2.18.3
[11] S4Vectors_0.22.1 BiocGenerics_0.30.0
[13] ggplot2_3.2.1
loaded via a namespace (and not attached):
[1] amap_0.8-18
[2] colorspace_1.4-1
[3] rjson_0.2.20
[4] hwriter_1.3.2
[5] XVector_0.24.0
[6] farver_2.0.1
[7] ggrepel_0.8.1
[8] bit64_0.9-7
[9] AnnotationDbi_1.46.1
[10] splines_3.6.1
[11] TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2
[12] zeallot_0.1.0
[13] Nozzle.R1_1.1-1
[14] Rsamtools_2.0.3
[15] annotate_1.62.0
[16] GO.db_3.8.2
[17] png_0.1-7
[18] pheatmap_1.0.12
[19] graph_1.62.0
[20] TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2
[21] compiler_3.6.1
[22] httr_1.4.1
[23] GOstats_2.50.0
[24] backports_1.1.5
[25] assertthat_0.2.1
[26] Matrix_1.2-17
[27] lazyeval_0.2.2
[28] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[29] limma_3.40.6
[30] prettyunits_1.1.0
[31] tools_3.6.1
[32] gtable_0.3.0
[33] glue_1.3.1
[34] GenomeInfoDbData_1.2.1
[35] Category_2.50.0
[36] reshape2_1.4.3
[37] systemPipeR_1.18.2
[38] dplyr_0.8.3
[39] batchtools_0.9.12
[40] rappdirs_0.3.1
[41] ShortRead_1.42.0
[42] Rcpp_1.0.3
[43] TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2
[44] TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2
[45] vctrs_0.2.1
[46] Biostrings_2.52.0
[47] gdata_2.18.0
[48] rtracklayer_1.44.4
[49] TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.7
[50] stringr_1.4.0
[51] lifecycle_0.1.0
[52] gtools_3.8.1
[53] XML_3.98-1.20
[54] edgeR_3.26.8
[55] zlibbioc_1.30.0
[56] scales_1.1.0
[57] BSgenome_1.52.0
[58] VariantAnnotation_1.30.1
[59] hms_0.5.3
[60] RBGL_1.60.0
[61] RColorBrewer_1.1-2
[62] yaml_2.2.0
[63] memoise_1.1.0
[64] biomaRt_2.40.5
[65] latticeExtra_0.6-29
[66] stringi_1.4.5
[67] RSQLite_2.2.0
[68] genefilter_1.66.0
[69] checkmate_1.9.4
[70] GenomicFeatures_1.36.4
[71] caTools_1.17.1.3
[72] chipseq_1.34.0
[73] rlang_0.4.2
[74] pkgconfig_2.0.3
[75] bitops_1.0-6
[76] TxDb.Celegans.UCSC.ce6.ensGene_3.2.2
[77] lattice_0.20-38
[78] purrr_0.3.3
[79] labeling_0.3
[80] GenomicAlignments_1.20.1
[81] bit_1.1-14
[82] tidyselect_0.2.5
[83] GSEABase_1.46.0
[84] AnnotationForge_1.26.0
[85] plyr_1.8.5
[86] magrittr_1.5
[87] R6_2.4.1
[88] gplots_3.0.1.1
[89] base64url_1.4
[90] DBI_1.1.0
[91] pillar_1.4.3
[92] withr_2.1.2
[93] survival_2.44-1.1
[94] RCurl_1.95-4.12
[95] tibble_2.1.3
[96] crayon_1.3.4
[97] KernSmooth_2.23-15
[98] jpeg_0.1-8.1
[99] progress_1.2.2
[100] locfit_1.5-9.1
[101] grid_3.6.1
[102] data.table_1.12.8
[103] blob_1.2.0
[104] Rgraphviz_2.28.0
[105] digest_0.6.23
[106] xtable_1.8-4
[107] brew_1.0-6
[108] munsell_0.5.0
Hi Nik,
Did you by any chance find a solution to this problem? My cross correlation plot is also empty, even though I do not get any error message.
Thanks, Steffi