Question: cmetindex missing in gmapr? Not possible to do bisulfite alignments
gravatar for karl.nordstroem
3 months ago by
karl.nordstroem0 wrote:

I wanted to generate bisulfite alignments with gmapR, but cannot get it to work. I can generate a normal alignment similar to how it is described in the documentation.

Running gsnap on the command line, you normally have to run cmetindex in order to prepare a normal genomic index for bisulfite alignments. Do you need to do this within gmapR as well?

Looking to the code-base, there are empty wrappers for both cmetindex and atoiindex. They are not visible within R. Is there a plan to add this functionality? Or am I just missing something obvious?


ADD COMMENTlink modified 3 months ago by Michael Lawrence9.9k • written 3 months ago by karl.nordstroem0
gravatar for Michael Lawrence
3 months ago by
United States
Michael Lawrence9.9k wrote:

I guess we were waiting for a post like this to motivate support for those. They look like they've been implemented, but they've never been tested. You could try calling them, passing the GmapGenome object. Let me know how it goes. Eventually we can export and document them.

ADD COMMENTlink written 3 months ago by Michael Lawrence9.9k


Well I'm working on my master thesis under supervision of Dr. Nordström, and I got your reply by email two days ago.

Actually I tried calling gmapR:::cmetindex(genome) and the result was like this:

Error in as.character.default(X[[i]], ...) :
   no method for coercing this S4 class to a vector

Any advice?
Thanks in advance



ADD REPLYlink written 3 months ago by Amer Ghalawinji0

gmapR 1.21.1 (devel) should resolve this issue by exporting cmetindex and adding the missing coercion.

ADD REPLYlink written 3 months ago by Michael Lawrence9.9k
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