genome searching with Biostrings and the BSgenome data packages
0
0
Entering edit mode
@mike_and_dan-10621
Last seen 8.0 years ago

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?

biostrings • 724 views
ADD COMMENT
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 470 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6