ChIPQC produces empty cross correlation plot
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Entering edit mode
@nikhilashokjoshi-19417
Last seen 18 months ago

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  
chipqc cross correlation • 162 views
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Entering edit mode

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

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