Question: Problem with importing bigWig file from GEO with rtracklayer?
4.3 years ago by
wrighth • 260
wrighth • 260 wrote:
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:  LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252  LC_MONETARY=English_United States.1252  LC_NUMERIC=C  LC_TIME=English_United States.1252 attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  rtracklayer_1.18.2 GenomicRanges_1.10.5 IRanges_1.16.4  BiocGenerics_0.4.0 loaded via a namespace (and not attached):  Biostrings_2.26.2 bitops_1.0-4.2 BSgenome_1.26.1 parallel_2.15.0  RCurl_1.95-3 Rsamtools_1.10.2 stats4_2.15.0 tools_2.15.0  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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