Missing some plots and columns in my ChIPQC report
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@mudithekanayake-22969
Last seen 17 months ago

Hello I'm trying to run ChIPQC on my data. After several attempts, finally I was able to get the final report. But some figures and some columns in tables are empty. Can someone help me with this issue. This is my datasheet.

SampleID    Factor  Replicate   bamReads    ControlID   bamControl  Peaks   PeakCaller  Tissue  Condition
K9_e9.5_Rep1    NA  1   data/bams/K9_S37_sorted.bam I1_Input1   data/bams/I1_S55_sorted.bam data/peakcalls/K9_peaks.narrowPeak  narrow  placenta    e9.5
K10_e9.5_Rep2   NA  2   data/bams/K10_S38_sorted.bam    I2_Input2   data/bams/I2_S56_sorted.bam data/peakcalls/K10_peaks.narrowPeak narrow  placenta    e9.5
K11_e9.5_Rep3   NA  3   data/bams/K11_S39_sorted.bam    I3_Input3   data/bams/I3_S57_sorted.bam data/peakcalls/K11_peaks.narrowPeak narrow  placenta    e9.5
K12_e9.5_Rep4   NA  4   data/bams/K12_S40_sorted.bam    I4_Input4   data/bams/I4_S58_sorted.bam data/peakcalls/K12_peaks.narrowPeak narrow  placenta    e9.5
K13_e9.5_Rep5   NA  5   data/bams/K13_S41_sorted.bam    I5_Input5   data/bams/I5_S59_sorted.bam data/peakcalls/K13_peaks.narrowPeak narrow  placenta    e9.5
K7_e9.5_Rep6    NA  6   data/bams/K7_S42_sorted.bam I6_Input6   data/bams/I6_S60_sorted.bam data/peakcalls/K7_peaks.narrowPeak  narrow  placenta    e9.5
K8_e7.5_Rep1    NA  1   data/bams/K8_S43_sorted.bam I7_Input1   data/bams/I7_S61_sorted.bam data/peakcalls/K8_peaks.narrowPeak  narrow  placenta    e7.5
K3_e7.5_Rep2    NA  2   data/bams/K3_S44_sorted.bam I8_Input2   data/bams/I8_S62_sorted.bam data/peakcalls/K3_peaks.narrowPeak  narrow  placenta    e7.5
K14_e7.5_Rep3   NA  3   data/bams/K14_S45_sorted.bam    I9_Input3   data/bams/I9_S63_sorted.bam data/peakcalls/K14_peaks.narrowPeak narrow  placenta    e7.5
K15_e7.5_Rep4   NA  4   data/bams/K15_S46_sorted.bam    I10_Input4  data/bams/I10_S64_sorted.bam    data/peakcalls/K15_peaks.narrowPeak narrow  placenta    e7.5
K16_e7.5_Rep5   NA  5   data/bams/K16_S47_sorted.bam    I11_Input5  data/bams/I11_S65_sorted.bam    data/peakcalls/K16_peaks.narrowPeak narrow  placenta    e7.5
K17_e7.5_Rep6   NA  6   data/bams/K17_S48_sorted.bam    I12_Input6  data/bams/I12_S66_sorted.bam    data/peakcalls/K17_peaks.narrowPeak narrow  placenta    e7.5
K18_e8.5_Rep1   NA  1   data/bams/K18_S49_sorted.bam    I13_Input1  data/bams/I13_S67_sorted.bam    data/peakcalls/K18_peaks.narrowPeak narrow  placenta    e8.5
K24_e8.5_Rep2   NA  2   data/bams/K24_S50_sorted.bam    I19_Input2  data/bams/I19_S68_sorted.bam    data/peakcalls/K24_peaks.narrowPeak narrow  placenta    e8.5
K20_e8.5_Rep3   NA  3   data/bams/K20_S51_sorted.bam    I15_Input3  data/bams/I15_S69_sorted.bam    data/peakcalls/K20_peaks.narrowPeak narrow  placenta    e8.5
K21_e8.5_Rep4   NA  4   data/bams/K21_S52_sorted.bam    I16_Input4  data/bams/I16_S70_sorted.bam    data/peakcalls/K21_peaks.narrowPeak narrow  placenta    e8.5
K22_e8.5_Rep5   NA  5   data/bams/K22_S53_sorted.bam    I17_Input5  data/bams/I17_S71_sorted.bam    data/peakcalls/K22_peaks.narrowPeak narrow  placenta    e8.5
K23_e8.5_Rep6   NA  6   data/bams/K23_S54_sorted.bam    I18_Input6  data/bams/I18_S72_sorted.bam    data/peakcalls/K23_peaks.narrowPeak narrow  placenta    e8.5

This is part of my table1 in the report. FragL and RelCC are empty. And also plot of CrossCoverage score after successive strand shifts is empty.

K10_e9.5_Rep2   placenta        e9.5    2   2902857 0   50  0   0   1.1 16
K11_e9.5_Rep3   placenta        e9.5    3   2302356 0   50  0   0   1   18
K12_e9.5_Rep4   placenta        e9.5    4   3436373 0   50  0   0   1.1 10
K13_e9.5_Rep5   placenta        e9.5    5   2099146 0   50  0   0   0.86    13
K14_e7.5_Rep3   placenta        e7.5    3   2393763 0   50  0   0   0.95    14
K15_e7.5_Rep4   placenta        e7.5    4   3157183 0   50  0   0   1.1 9.3
K16_e7.5_Rep5   placenta        e7.5    5   3012725 0   50  0   0   1.1 18
K17_e7.5_Rep6   placenta        e7.5    6   2340808 0   50  0   0   1.2 1.3
K18_e8.5_Rep1   placenta        e8.5    1   2335214 0   50  0   0   1.2 1.5
K20_e8.5_Rep3   placenta        e8.5    3   2538516 0   50  0   0   1.2 2
K21_e8.5_Rep4   placenta        e8.5    4   2702481 0   50  0   0   0.98    12
K22_e8.5_Rep5   placenta        e8.5    5   2465993 0   50  0   0   0.96    10
K23_e8.5_Rep6   placenta        e8.5    6   2406749 0   50  0   0   1.1 14
K24_e8.5_Rep2   placenta        e8.5    2   2130250 0   50  0   0   0.85    11
K3_e7.5_Rep2    placenta        e7.5    2   2213102 0   50  0   0   1.2 20
K7_e9.5_Rep6    placenta        e9.5    6   1941471 0   50  0   0   1   16
K8_e7.5_Rep1    placenta        e7.5    1   2927401 0   50  0   0   1.3 19
K9_e9.5_Rep1    placenta        e9.5    1   2170794 0   50  0   0   0.83    10
I9_Input3   NA  NA  NA  NA  1816228 0   50  0   0   0.83    NA
I10_Input4  NA  NA  NA  NA  2274787 0   50  0   0   0.89    NA
I11_Input5  NA  NA  NA  NA  3328915 0   50  0   0   1.3 NA
I12_Input6  NA  NA  NA  NA  2535485 0   50  0   0   1   NA
I13_Input1  NA  NA  NA  NA  3542427 0   50  0   0   1   NA
I1_Input1   NA  NA  NA  NA  2650131 0   50  0   0   1.1 NA
I2_Input2   NA  NA  NA  NA  3263128 0   50  0   0   1.4 NA

These are my commands.

library(ChIPQC)
samples <- read.csv('meta/chip-seq_metadata.csv')
register(SerialParam())
chipObj <- ChIPQC(samples, annotation="mm10")
ChIPQCreport(chipObj, reportName="ChIP QC report: Nanog and Pou5f1", reportFolder="ChIPQCreport")

This is session info.

> sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

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] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] ChIPQC_1.21.0               DiffBind_2.14.0             SummarizedExperiment_1.16.1
 [4] DelayedArray_0.12.2         BiocParallel_1.20.1         matrixStats_0.55.0         
 [7] Biobase_2.46.0              GenomicRanges_1.38.0        GenomeInfoDb_1.22.0        
[10] IRanges_2.20.2              S4Vectors_0.24.3            BiocGenerics_0.32.0        
[13] ggplot2_3.2.1               devtools_2.2.2              usethis_1.5.1              
[16] BiocManager_1.30.10        

loaded via a namespace (and not attached):
  [1] backports_1.1.5                           GOstats_2.52.0                           
  [3] BiocFileCache_1.10.2                      plyr_1.8.5                               
  [5] lazyeval_0.2.2                            GSEABase_1.48.0                          
  [7] splines_3.6.2                             amap_0.8-18                              
  [9] digest_0.6.25                             GO.db_3.10.0                             
 [11] gdata_2.18.0                              fansi_0.4.1                              
 [13] magrittr_1.5                              checkmate_2.0.0                          
 [15] memoise_1.1.0                             BSgenome_1.54.0                          
 [17] base64url_1.4                             limma_3.42.2                             
 [19] remotes_2.1.1                             Biostrings_2.54.0                        
 [21] annotate_1.64.0                           Nozzle.R1_1.1-1                          
 [23] systemPipeR_1.20.0                        askpass_1.1                              
 [25] prettyunits_1.1.1                         jpeg_0.1-8.1                             
 [27] colorspace_1.4-1                          blob_1.2.1                               
 [29] rappdirs_0.3.1                            ggrepel_0.8.1                            
 [31] dplyr_0.8.4                               callr_3.4.2                              
 [33] crayon_1.3.4                              RCurl_1.98-1.1                           
 [35] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2   graph_1.64.0                             
 [37] chipseq_1.36.0                            genefilter_1.68.0                        
 [39] brew_1.0-6                                survival_3.1-8                           
 [41] VariantAnnotation_1.32.0                  glue_1.3.1                               
 [43] gtable_0.3.0                              zlibbioc_1.32.0                          
 [45] XVector_0.26.0                            pkgbuild_1.0.6                           
 [47] Rgraphviz_2.30.0                          scales_1.1.0                             
 [49] pheatmap_1.0.12                           DBI_1.1.0                                
 [51] edgeR_3.28.0                              TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2  
 [53] Rcpp_1.0.3                                xtable_1.8-4                             
 [55] progress_1.2.2                            bit_1.1-15.2                             
 [57] AnnotationForge_1.28.0                    httr_1.4.1                               
 [59] gplots_3.0.1.2                            RColorBrewer_1.1-2                       
 [61] ellipsis_0.3.0                            farver_2.0.3                             
 [63] pkgconfig_2.0.3                           XML_3.99-0.3                             
 [65] dbplyr_1.4.2                              locfit_1.5-9.1                           
 [67] labeling_0.3                              tidyselect_1.0.0                         
 [69] rlang_0.4.4                               reshape2_1.4.3                           
 [71] AnnotationDbi_1.48.0                      munsell_0.5.0                            
 [73] tools_3.6.2                               cli_2.0.1                                
 [75] RSQLite_2.2.0                             stringr_1.4.0                            
 [77] yaml_2.2.1                                processx_3.4.2                           
 [79] bit64_0.9-7                               fs_1.3.1                                 
 [81] caTools_1.18.0                            purrr_0.3.3                              
 [83] RBGL_1.62.1                               TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2  
 [85] biomaRt_2.42.0                            compiler_3.6.2                           
 [87] rstudioapi_0.11                           curl_4.3                                 
 [89] png_0.1-7                                 testthat_2.3.1                           
 [91] tibble_2.1.3                              stringi_1.4.6                            
 [93] ps_1.3.2                                  GenomicFeatures_1.38.2                   
 [95] desc_1.2.0                                TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2  
 [97] lattice_0.20-38                           Matrix_1.2-18                            
 [99] vctrs_0.2.3                               pillar_1.4.3                             
[101] lifecycle_0.1.0                           data.table_1.12.8                        
[103] bitops_1.0-6                              TxDb.Mmusculus.UCSC.mm10.knownGene_3.10.0
[105] TxDb.Celegans.UCSC.ce6.ensGene_3.2.2      rtracklayer_1.46.0                       
[107] R6_2.4.1                                  latticeExtra_0.6-29                      
[109] hwriter_1.3.2                             ShortRead_1.44.3                         
[111] KernSmooth_2.23-16                        sessioninfo_1.1.1                        
[113] gtools_3.8.1                              assertthat_0.2.1                         
[115] pkgload_1.0.2                             openssl_1.4.1                            
[117] Category_2.52.1                           rprojroot_1.3-2                          
[119] rjson_0.2.20                              withr_2.1.2                              
[121] GenomicAlignments_1.22.1                  batchtools_0.9.12                        
[123] Rsamtools_2.2.2                           GenomeInfoDbData_1.2.2                   
[125] hms_0.5.3                                 grid_3.6.2                               
[127] TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2
ChIPQC BioConductor • 128 views
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