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Question: genome searching with Biostrings and the BSgenome data packages
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gravatar for mike_and_dan
19 months ago by
mike_and_dan0 wrote:

Hello

I have been attempting to perform genome searching using the vignette:  Efficient genome searching with Biostrings and the BSgenome data packages.  

I do not receive an error when follow the vignette using the C elegans genome that is used in the example .  When change the genome to D rerio and include a single DNA sequence (as an XStringviews) to search I get the following:

Error in normargPattern(pattern, subject) : 
'pattern' must be a single string or an XString object

from normargPattern (Biostrings) ciring

else if (!isSingleString(pattern)) 
stop("'", argname, "' must be a single string or an XString object")

 

when I test the isSingleString function, the response is TRUE.

Any suggestion on how to get past this?

ADD COMMENTlink modified 19 months ago by Martin Morgan ♦♦ 21k • written 19 months ago by mike_and_dan0

You need to give a simple, reproducible example of what is not working for you. Otherwise all we know is that you did something and it didn't work.

ADD REPLYlink written 19 months ago by James W. MacDonald45k
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