Hello
I have several bigWig files from a ChIP-Seq expeiment. The files were generated in Galaxy using MACS and then converted from wig to bigwig using galaxy's Wig/BedGraph-to-bigWig converter.
When I attempt to import these bigwigs into R using the import.bw function I get the following error:
udc couldn't read 4 bytes from Galaxy215-[167_phage_input_Wig_BedGraph-to-bigWig].bigwig, did read 0
I suppose this is something rather stupid, but I'm not sure what may be the source of the problem or how to start troubleshooting this.
Does anyone has any idea what may cause this?
Thanks in advance
Dolev Rahat
sessionInfo:
R version 3.1.1 (2014-07-10)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] rtracklayer_1.26.2 GenomicRanges_1.18.4 GenomeInfoDb_1.2.4
[4] IRanges_2.0.1 S4Vectors_0.4.0 BiocGenerics_0.12.1
loaded via a namespace (and not attached):
[1] BBmisc_1.8 BatchJobs_1.5 BiocParallel_1.0.2
[4] Biostrings_2.34.1 DBI_0.3.1 GenomicAlignments_1.2.1
[7] RCurl_1.95-4.5 RSQLite_1.0.0 Rsamtools_1.18.3
[10] XML_3.98-1.1 XVector_0.6.0 base64enc_0.1-2
[13] bitops_1.0-6 brew_1.0-6 checkmate_1.5.1
[16] codetools_0.2-8 digest_0.6.8 fail_1.2
[19] foreach_1.4.2 iterators_1.0.7 sendmailR_1.2-1
[22] stringr_0.6.2 tools_3.1.1 zlibbioc_1.12.0
What's the size of the .bigwig file you are trying to read in? What does the first line look like?
@ Dan TenenbaumThe file size is about 29Mb. Iv'e intially tried to open only a subset of it using the which option with a GRanges object, but I get the error message regardless to whether I use which or not.
From what I can see In Galaxy the first line is
line 31798454 of stdin: chromosome chr5 has 152537259 bases, but item ends at 152537260 line 34647404 of stdin: chromosome chr13 has 120284312 bases, but item ends at 120284320 line 34647405 of stdin: chromosome chr13 has 120284312 bases