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Question: Problem with importing bigWig file from GEO with rtracklayer?
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gravatar for wrighth
3.8 years ago by
wrighth260
wrighth260 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: [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
ADD COMMENTlink modified 3.8 years ago by Dario Strbenac1.3k • written 3.8 years ago by wrighth260
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gravatar for Dario Strbenac
3.8 years ago by
Dario Strbenac1.3k
Australia
Dario Strbenac1.3k wrote:
rtracklayer can't read bigWig files on a Windows computer. Type in ?`BigWigFile-class` to get the help file where it explains this. It would be lovely if it could. ________________________________________ From: bioconductor-bounces@r-project.org [bioconductor- bounces@r-project.org] on behalf of Hollis Wright [wrighth@ohsu.edu] Sent: Thursday, 15 August 2013 6:11 AM To: bioconductor at r-project.org Subject: [BioC] Problem with importing bigWig file from GEO with rtracklayer? 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 _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 3.8 years ago by Dario Strbenac1.3k
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