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Question: plotTracks issue with BAM files (ChIP-seq, paired)
1
gravatar for kevin.rue
5 months ago by
kevin.rue220
University of Oxford
kevin.rue220 wrote:

Hello!

I am trying to plotTracks reads mapped to a ChIP-seq peak region for a set of 6 BAM files (3 ChIP, 3 inputs) that contain paired-end reads. If I subset to certain samples, it works as per this screenshot: https://www.dropbox.com/s/s71s9wu8v8vpshb/Screenshot%202018-06-19%2014.09.19.png?dl=1

However, certain samples (1 ChIP, 2 inputs) cause the error:

Error in .normarg_at2(at, x) : some ranges in 'at' are off-limits with respect to their corresponding sequence in 'x'

It's a bit challenging to share a minimal reproducible example in the post, so I have linked to my public Dropbox for now.
https://www.dropbox.com/s/htpmsqfadut3iyr/Gviz.zip?dl=1

This link points to a ZIP archive (13 KB) that contains small files to reproduce my issue:

  • region.bed: the peak region
  • subset.bam and the accompanying *bai index: reads that overlap the region defined above. I generated those files using bedtools intersect to produce a small file that I can share to reproduce the issue.
    • Note that this file produces the exact same error as the full-size file, even though it probable misses some reads outside the region that are paired with a mate inside the region.
  • issue.R: an R script that uses the files above and produces the error.

For the record, issue.R looks like this:

require(rtracklayer)
topRegion <- import.bed("region.bed")
require(Rsamtools)
sbp <- ScanBamParam(
    which=GRanges(
        seqnames = seqnames(topRegion),
        ranges=IRanges(
            start=start(topRegion)-width(topRegion),
            end = end(topRegion)+width(topRegion))
        )
    )
require(Gviz)
testTrack <- AlignmentsTrack("subset.bam", isPaired=TRUE, name = "Test")
plotTracks(
    list(testTrack),
    from=start(topRegion),
    to=end(topRegion),
    chromosome=seqnames(topRegion),
    extend.left = width(topRegion),
    extend.right = width(topRegion))​

 

Here is the stack trace that I can see in RStudio:

 Error in .normarg_at2(at, x) : 
  some ranges in 'at' are off-limits with respect to their corresponding sequence in 'x' 
21.
stop(.wrap_msg("some ranges in 'at' are off-limits with respect to ", 
    "their corresponding sequence in 'x'")) 
20.
.normarg_at2(at, x) 
19.
replaceAt(x, at, value = value) 
18.
replaceAt(x, at, value = value) 
17.
sequenceLayer(reads$seq, reads$cigar) 
16.
x@stream(x@reference, subRegion) 
15.
mcols(data) 
14.
colnames(mcols(data)) 
13.
eval(quote(list(...)), env) 
12.
eval(quote(list(...)), env) 
11.
eval(quote(list(...)), env) 
10.
standardGeneric("paste") 
9.
paste(colnames(mcols(data)), "orig", sep = "__.__") 
8.
.resolveColMapping(x@stream(x@reference, subRegion), x@args, 
    x@mapping) 
7.
.local(x, ...) 
6.
subset(x, from = from, to = to, chromosome = chromosome, sort = FALSE, 
    stacks = FALSE, use.defaults = FALSE) 
5.
subset(x, from = from, to = to, chromosome = chromosome, sort = FALSE, 
    stacks = FALSE, use.defaults = FALSE) 
4.
FUN(X[[i]], ...) 
3.
lapply(trackList, function(x) {
    chromosome(x) <- chromosome
    subset(x, from = from, to = to, chromosome = chromosome, 
        sort = FALSE, stacks = FALSE, use.defaults = FALSE) ... 
2.
lapply(trackList, function(x) {
    chromosome(x) <- chromosome
    subset(x, from = from, to = to, chromosome = chromosome, 
        sort = FALSE, stacks = FALSE, use.defaults = FALSE) ... 
1.
plotTracks(list(testTrack), from = start(topRegion), to = end(topRegion), 
    chromosome = seqnames(topRegion), extend.left = width(topRegion), 
    extend.right = width(topRegion)) 

Here is my session information:

> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.5

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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

other attached packages:
 [1] Gviz_1.24.0          Rsamtools_1.32.0     Biostrings_2.48.0    XVector_0.20.0       rtracklayer_1.40.3  
 [6] GenomicRanges_1.32.3 GenomeInfoDb_1.16.0  IRanges_2.14.10      S4Vectors_0.18.3     BiocGenerics_0.26.0 

loaded via a namespace (and not attached):
 [1] Biobase_2.40.0              httr_1.3.1                  bit64_0.9-7                 splines_3.5.0              
 [5] Formula_1.2-3               assertthat_0.2.0            latticeExtra_0.6-28         blob_1.1.1                 
 [9] BSgenome_1.48.0             GenomeInfoDbData_1.1.0      yaml_2.1.19                 progress_1.1.2             
[13] pillar_1.2.3                RSQLite_2.1.1               backports_1.1.2             lattice_0.20-35            
[17] biovizBase_1.28.0           digest_0.6.15               RColorBrewer_1.1-2          checkmate_1.8.5            
[21] colorspace_1.3-2            htmltools_0.3.6             Matrix_1.2-14               plyr_1.8.4                 
[25] XML_3.98-1.11               biomaRt_2.36.1              zlibbioc_1.26.0             scales_0.5.0               
[29] BiocParallel_1.14.1         htmlTable_1.12              tibble_1.4.2                AnnotationFilter_1.4.0     
[33] ggplot2_2.2.1               SummarizedExperiment_1.10.1 GenomicFeatures_1.32.0      nnet_7.3-12                
[37] lazyeval_0.2.1              survival_2.42-3             magrittr_1.5                memoise_1.1.0              
[41] foreign_0.8-70              tools_3.5.0                 data.table_1.11.4           prettyunits_1.0.2          
[45] matrixStats_0.53.1          stringr_1.3.1               munsell_0.4.3               cluster_2.0.7-1            
[49] DelayedArray_0.6.0          AnnotationDbi_1.42.1        ensembldb_2.4.1             compiler_3.5.0             
[53] rlang_0.2.1                 RCurl_1.95-4.10             dichromat_2.0-0             rstudioapi_0.7             
[57] VariantAnnotation_1.26.0    htmlwidgets_1.2             bitops_1.0-6                base64enc_0.1-3            
[61] gtable_0.2.0                curl_3.2                    DBI_1.0.0                   R6_2.2.2                   
[65] GenomicAlignments_1.16.0    gridExtra_2.3               knitr_1.20                  bit_1.1-14                 
[69] Hmisc_4.1-1                 ProtGenerics_1.12.0         stringi_1.2.2               Rcpp_0.12.17               
[73] rpart_4.1-13                acepack_1.4.1              

 

ADD COMMENTlink modified 5 months ago • written 5 months ago by kevin.rue220

I just realized I just posted almost exactly the same question here: Gviz Alignment Tracks with non-UCSC reference chromosome names

ADD REPLYlink written 9 weeks ago by laura.k.hilton0
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