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Question: cmetindex missing in gmapr? Not possible to do bisulfite alignments
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gravatar for karl.nordstroem
12 days 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 12 days ago by Michael Lawrence9.8k • written 12 days ago by karl.nordstroem0
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gravatar for Michael Lawrence
12 days ago by
United States
Michael Lawrence9.8k 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 12 days ago by Michael Lawrence9.8k

Hey!

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

Best,

Amer

ADD REPLYlink written 9 days ago by Amer Ghalawinji0

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

ADD REPLYlink written 7 days ago by Michael Lawrence9.8k
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