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mudithekanayake
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@mudithekanayake-22969
Last seen 4.7 years 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
