Question

ChIPQC failed on chrM

0

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seasky002002 • 0

@seasky002002-13307

Last seen 7.4 years ago

Hi,

I encountered an error while using ChIPQC. It reported an error after calculation shift for chrM. I pasted the error message below. It looks like happened on chrM, so i change the parameter chromosomes to exclude chrM, and the ChIPQC program run successfully.

But i still curious why the error happened on chrM. Would someone can give me an answer?

Thank you!

The error message:

Calculating shift for chrM

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Error in names(res) <- nms :
'names' attribute [18] must be the same length as the vector [1]
Calls: ChIPQC -> bplapply -> bplapply -> bplapply -> bplapply

ChIPQC • 1.8k views

ADD COMMENT • link updated 7.4 years ago by Thomas Carroll ▴ 420 • written 7.4 years ago by seasky002002 • 0

0

Entering edit mode

Hello

I get this same error at the start of my run. Was there a solution to this? My sessionInfo is attached below but also I get a message when I load the library, not sure if this has anything to do with it: No methods found in "RSQLite" for requests: dbGetQuery

Bam file has 93 contigs

Error in names(res) <- nms : 
  'names' attribute [28] must be the same length as the vector [4]
Calls: ChIPQC -> bplapply -> bplapply -> bplapply -> bplapply

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.8 (Final)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] ChIPQC_1.10.3              DiffBind_2.2.12           
 [3] SummarizedExperiment_1.4.0 Biobase_2.34.0            
 [5] GenomicRanges_1.26.4       GenomeInfoDb_1.10.3       
 [7] IRanges_2.8.2              S4Vectors_0.12.2          
 [9] BiocGenerics_0.20.0        ggplot2_2.2.1

ADD REPLY • link 7.3 years ago meeta.mistry ▴ 30

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Entering edit mode

hi,

The original error looks to do with the way ChIPQC calculates cross coverage. The ChrM may cause some problems here because it is circular.

I believe there is a way to check for circular chromosomes so I will look to remove any circular chromosomes while providing a warning for the user.

For now the solution is to remove the mitochondrial chromosome.

I usually provide ChIPQC with a vector of the main chromosomes omitting ChrM and the contigs which haven't been fully assembled into main chromosomes.

Something like

> chromosomesToTest <- c(paste0("chr",c(1:22,"X","Y")))

> chromosomesToTest
[1] "chr1" "chr2" "chr3" "chr4" "chr5" "chr6" "chr7" "chr8" "chr9" "chr10" "chr11" "chr12"
[13] "chr13" "chr14" "chr15" "chr16" "chr17" "chr18" "chr19" "chr20" "chr21" "chr22" "chrX" "chrY"

> my_experiment = ChIPQC(experiment="CellLine_Experiment_Sheet.csv", annotation="hg19",chromosomes=chromosomesToTest)

I will look to update ChIPQC to remove the ChrM internally in the next version.

best,

tom

ADD REPLY • link 7.3 years ago Thomas Carroll ▴ 420

score 0 · Answer 1 · 2017-06-26

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Entering edit mode

Thomas Carroll ▴ 420

@thomas-carroll-7019

Last seen 2.0 years ago

United States/New York/The Rockefeller …

hi,

Could you let me know what version of ChIPQC you are using? The result from a call to sessionInfo() should be good.

best,

tom

ADD COMMENT • link 7.4 years ago Thomas Carroll ▴ 420