EMIRGE method choice

[domenico-simone]

Hello,

I would like to try EMIRGE on metatranscriptome reads. Indeed I have already sorted the putative SSU reads out with cmsearch. Would you suggest using the normal EMIRGE version or the amplicon variant?

Thanks,
Domenico

[csmiller]

I'd recommend the amplicon version for speed, but you might have to restrict the run to a few million reads depending on RAM and patience. If you try this and have other insights or suggestions, let everyone know here:
https://groups.google.com/group/emirge-users
Chris