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Question: biostrings report "XStringSet object is too big to be unlisted" error
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gravatar for zwfanwz678
3 months ago by
zwfanwz6780
zwfanwz6780 wrote:

hello everone,

I using Biostrings::readDNAStringSet to cut some sequence from hg19.fa, but an error occurs when I run the program(as follows).

seq <- Biostrings::readDNAStringSet("hg19.fa")
genome <- GenomeInfoDb::Seqinfo(genome = NA_character_)
gr_a <- BiocGenerics::unstrand(rtracklayer::import("file.bed", genome = genome))
a <- seq[gr_a]

gr_a is a GRanges object, when run a <- seq[gr_a], R report

"Error in .Call2("XStringSet_unlist", x, PACKAGE = "Biostrings") : 
  XStringSet object is too big to be unlisted (would result in an XString
  object of length 2^31 or more)"

I try these codes several times, but sometimes the code runs very well, sometimes it report the error above.

what's wrong with these code?

thanks!

ADD COMMENTlink written 3 months ago by zwfanwz6780
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