[BioC] Problem with importing bigWig file from GEO with rtracklayer?
Hollis Wright
wrighth at ohsu.edu
Wed Aug 14 22:11:31 CEST 2013
Hi; I'm using rtracklayer to try to read in a bigWig file from a GEO dataset so I can overlay it on some existing data we have in GenomicRanges objects. Unfortunately, I keep running into the same error:
bw <- import(con="GSM1115998_Groseq-MCF7-EtoH-rep2.minusstrand.bigWig", format="bigWig")
Error in seqinfo(ranges) : UCSC library operation failed
In addition: Warning message:
In seqinfo(ranges) : End of file reading 4096 bytes (got 939)
I initially thought this was a problem with the file being corrupted, but I've both re-downloaded the archive and tried other files from it and received the same error every time. Any thoughts? sessionInfo below:
R version 2.15.0 (2012-03-30)
Platform: x86_64-pc-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rtracklayer_1.18.2 GenomicRanges_1.10.5 IRanges_1.16.4
[4] BiocGenerics_0.4.0
loaded via a namespace (and not attached):
[1] Biostrings_2.26.2 bitops_1.0-4.2 BSgenome_1.26.1 parallel_2.15.0
[5] RCurl_1.95-3 Rsamtools_1.10.2 stats4_2.15.0 tools_2.15.0
[9] XML_3.95-0.1 zlibbioc_1.4.0
Thanks!
Hollis Wright, PhD
Ojeda Lab, Division of Neuroscience
Oregon Health and Science University
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