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zebasilio
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@zebasilio-19655
Last seen 4.1 years ago
Hi!!
I am using ChipQC to check for the quality of a Chipseq experiment we performed in our lab. We have 12 samples (4x input controls, 4x ChipA, 4x ChipB), but unfortunately I get always an error message. Code, error message and session information can be seen below. I thank you in advance for any help you can provide. José
> samples<-read.csv("samples_datasheet.csv")
> BlacklistFile<-"/media/jose/Volume/annotation/black_list/ENCFF001TDO.bed"
#(BlacklistFile downloaded from: ENCFF001TDO (h19 assembly): https://www.encodeproject.org/annotations/ENCSR636HFF/)
> moser_chipseq = ChIPQC(samples,
+ annotation="hg19",
+ blacklist = BlacklistFile, chromosomes=NULL)
Myc_A Hela_cells Myc Myc Myc 1 bed
Myc_B Hela_cells Myc Myc Myc 2 bed
Myc_C Hela_cells Myc Myc Myc 3 bed
Myc_D Hela_cells Myc Myc Myc 4 bed
IKK1_A Hela_cells IKK1 IKK1 IKK1 1 bed
IKK1_B Hela_cells IKK1 IKK1 IKK1 2 bed
IKK1_C Hela_cells IKK1 IKK1 IKK1 3 bed
IKK1_D Hela_cells IKK1 IKK1 IKK1 4 bed
Compiling annotation...
Computing metrics for 12 samples...
list
Bam file has 25 contigs
Calculating coverage histogram for chr1
Calculating SSD for chr1
Calculating unique positions per strand for chr1
Calculating shift for chr1
300 / 300
Counting reads in features for chr1
Signal over peaks for chr1
done
Calculating coverage
Calculating Summits on chr1 ..Calculating coverage histogram for chr2
Calculating SSD for chr2
Calculating unique positions per strand for chr2
Calculating shift for chr2
300 / 300
Counting reads in features for chr2
Signal over peaks for chr2
done
Calculating coverage
Calculating Summits on chr2 ..Calculating coverage histogram for chr3
Calculating SSD for chr3
Calculating unique positions per strand for chr3
Calculating shift for chr3
11list300
Bam file has 25 contigs
Calculating coverage histogram for chr1
Calculating SSD for chr1
Calculating unique positions per strand for chr1
Calculating shift for chr1
300 / 300
Counting reads in features for chr1
Signal over peaks for chr1
done
Calculating coverage
Calculating Summits on chr1 ..Calculating coverage histogram for chr2
Calculating SSD for chr2
Calculating unique positions per strand for chr2
Calculating shift for chr2
300 / 300
Counting reads in features for chr2
Signal over peaks for chr2
done
Calculating coverage
Calculating coverage histogram for chr3
Calculating SSD for chr3
Calculating unique positions per strand for chr3
Calculating shift for chr3
**1Error in 1:(2 * readlength(object)) : NA/NaN argument**
> sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.1 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=de_AT.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=de_AT.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=de_AT.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=de_AT.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] ChIPQC_1.18.0 DiffBind_2.10.0 SummarizedExperiment_1.12.0 DelayedArray_0.8.0 BiocParallel_1.16.2 matrixStats_0.54.0
[7] Biobase_2.42.0 GenomicRanges_1.34.0 GenomeInfoDb_1.18.1 IRanges_2.16.0 S4Vectors_0.20.1 BiocGenerics_0.28.0
[13] ggplot2_3.1.0
loaded via a namespace (and not attached):
[1] backports_1.1.2 ChIPseeker_1.18.0 GOstats_2.48.0 fastmatch_1.1-0
[5] plyr_1.8.4 igraph_1.2.2 lazyeval_0.2.1 GSEABase_1.44.0
[9] splines_3.5.2 BatchJobs_1.7 gridBase_0.4-7 urltools_1.7.1
[13] amap_0.8-16 digest_0.6.18 GOSemSim_2.8.0 viridis_0.5.1
[17] GO.db_3.7.0 gdata_2.18.0 magrittr_1.5 checkmate_1.8.5
[21] memoise_1.1.0 BBmisc_1.11 limma_3.38.3 Nozzle.R1_1.1-1
[25] Biostrings_2.50.1 annotate_1.60.0 systemPipeR_1.16.0 enrichplot_1.2.0
[29] prettyunits_1.0.2 colorspace_1.3-2 blob_1.1.1 ggrepel_0.8.0
[33] dplyr_0.7.8 crayon_1.3.4 RCurl_1.95-4.11 jsonlite_1.6
[37] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 graph_1.60.0 chipseq_1.32.0 genefilter_1.64.0
[41] bindr_0.1.1 sendmailR_1.2-1 brew_1.0-6 survival_2.43-3
[45] glue_1.3.0 gtable_0.2.0 zlibbioc_1.28.0 XVector_0.22.0
[49] UpSetR_1.3.3 Rgraphviz_2.26.0 scales_1.0.0 DOSE_3.8.0
[53] pheatmap_1.0.10 DBI_1.0.0 edgeR_3.24.1 TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2
[57] Rcpp_1.0.0 plotrix_3.7-4 viridisLite_0.3.0 xtable_1.8-3
[61] progress_1.2.0 units_0.6-2 gridGraphics_0.3-0 bit_1.1-14
[65] europepmc_0.3 AnnotationForge_1.24.0 httr_1.4.0 fgsea_1.8.0
[69] gplots_3.0.1 RColorBrewer_1.1-2 pkgconfig_2.0.2 XML_3.98-1.16
[73] farver_1.1.0 locfit_1.5-9.1 ggplotify_0.0.3 tidyselect_0.2.5
[77] rlang_0.3.0.1 reshape2_1.4.3 AnnotationDbi_1.44.0 munsell_0.5.0
[81] tools_3.5.2 RSQLite_2.1.1 ggridges_0.5.1 stringr_1.3.1
[85] bit64_0.9-7 caTools_1.17.1.1 purrr_0.2.5 ggraph_1.0.2
[89] bindrcpp_0.2.2 RBGL_1.58.1 TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2 DO.db_2.9
[93] xml2_1.2.0 biomaRt_2.38.0 compiler_3.5.2 rstudioapi_0.8
[97] tibble_1.4.2 tweenr_1.0.0 stringi_1.2.4 TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2
[101] GenomicFeatures_1.34.1 lattice_0.20-38 Matrix_1.2-15 pillar_1.3.0
[105] BiocManager_1.30.4 triebeard_0.3.0 TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.4 data.table_1.11.8
[109] cowplot_0.9.3 bitops_1.0-6 TxDb.Celegans.UCSC.ce6.ensGene_3.2.2 rtracklayer_1.42.1
[113] qvalue_2.14.0 R6_2.3.0 latticeExtra_0.6-28 hwriter_1.3.2
[117] ShortRead_1.40.0 KernSmooth_2.23-15 gridExtra_2.3 boot_1.3-20
[121] MASS_7.3-51.1 gtools_3.8.1 assertthat_0.2.0 Category_2.48.0
[125] rjson_0.2.20 withr_2.1.2 GenomicAlignments_1.18.0 Rsamtools_1.34.0
[129] GenomeInfoDbData_1.2.0 hms_0.4.2 grid_3.5.2 TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2
[133] rvcheck_0.1.3 ggforce_0.1.3 base64enc_0.1-3
Does anyone have any idea how could I solve this? Any help is very appreciated. Best, José
hi,
I suspect this may be caused by some peaks being very close to chromosome start or ends. I will put in a fix for this case tonight and that may solve this issue. Would you be able to share your bed files with me? If you can send a link to me at tcarroll(at)rockefeller.edu, then I could test that this solved the problem.
Thanks,
tom
hi,
I suspect this may be caused by some peaks being very close to chromosome start or ends. I will put in a fix for this case tonight and that may solve this issue. Would you be able to share your bed files with me? If you can send a link to me at tcarroll(at)rockefeller.edu, then I could test that this solved the problem.
Thanks,
tom
Dear Prof. Carroll, I have sent you the bed files as you requested.
Thank you so much for your effort. Best Regards, José Basílio
hi, I have added some code to remove peaks close to chromosome edges (within distance of window defined in profileWin parameter) and report number removed. Hopefully this is the issue.
This is in release ChIPQC version 1.18.2.
thank you for report,
tom
hi, I have added some code to remove peaks close to chromosome edges (within distance of window defined in profileWin parameter) and report number removed. Hopefully this is the issue.
This is in release ChIPQC version 1.18.2.
thank you for report,
tom