Question: rtracklayer - bug
gravatar for story.benjamin
19 months ago by
story.benjamin0 wrote:


A colleague approached me in hopes of figuring out a strange export problem they were having with rtracklayer. For some reason it seems that when I have over 255-256 chromosomes (manual tested this) in a genome, that certain chromosome(s) are lost during the export of a bigwig.

This was noticed by said colleague as they loaded a rtracklayer generated bigWig into IGV and the X chromosome was missing. 

Here is the code being run:

gr <- readGAlignments('Downloads/A250_S1_001_subset.bam')
seqlevelsStyle(gr) <- 'UCSC'

gg <- coverage( gr )

gg$chrX,'') <- import('')
coverage( )$chrX

Here is the output:

> library(GenomicAlignments)
> library(rtracklayer)
> gr <- readGAlignments('Downloads/A250_Wills_S1_001_subset.bam')
> seqlevelsStyle(gr) <- 'UCSC'
> gg <- coverage( gr )
> gg$chrX
integer-Rle of length 123869142 with 177 runs
  Lengths:  488442      74       8      75  499789       1 ...  540531      74     172      73 1743866
  Values :       0       1       0       1       0       1 ...       0       1       0       1       0
> <- import('')
> coverage( )$chrX
integer-Rle of length 123869142 with 1 run
  Lengths: 123869142
  Values :         0

As you can see somehow the X chromosome has lost al of its coverage information? However it can be noted that if we subset the coverage object (gg) to a list of coverages with less than about 255 chromosomes then the X chromosome coverage returns in the bigwig generated during the "" step. Currently, we have a 2422 chromosomes (based on the seqinfo call) with no seqlengths provided. As a side note, other chromosomes seem to keep their correct coverage values in the bigwig.




R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.9.5 (Mavericks)

[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] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] rtracklayer_1.32.2         GenomicAlignments_1.8.4    Rsamtools_1.24.0           Biostrings_2.40.2          XVector_0.12.1            
 [6] SummarizedExperiment_1.2.3 Biobase_2.32.0             GenomicRanges_1.24.3       GenomeInfoDb_1.8.7         IRanges_2.6.1             
[11] S4Vectors_0.10.3           BiocGenerics_0.18.0       

loaded via a namespace (and not attached):
[1] XML_3.98-1.4       bitops_1.0-6       zlibbioc_1.18.0    BiocParallel_1.6.6 tools_3.3.1        RCurl_1.95-4.8    

ADD COMMENTlink modified 19 months ago by Michael Lawrence10.0k • written 19 months ago by story.benjamin0
gravatar for Michael Lawrence
19 months ago by
Michael Lawrence10.0k
United States
Michael Lawrence10.0k wrote:

I think I fixed this in 1.35.1. It appears that the Kent library assumes that the blockSize is >= the number of chromosomes. It looks like even the wig2bigwig command line tool expects the user to manually override that setting in the >256 chromosome case.

ADD COMMENTlink written 19 months ago by Michael Lawrence10.0k

Is there a way to download version 1.35.1? and or a work around hack to get this to work under current framework? I'm having a similar problem that is affecting pipelines but the latest update of rtracklayer is 1.34.0

ADD REPLYlink written 19 months ago by chitsazanalex0

It will be in 1.34.1

ADD REPLYlink written 19 months ago by Michael Lawrence10.0k
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