This metagenomics publication from our team a few years ago took a
somewhat similar approach. Perhaps it can be adapted?
I am trying to perform metatranscriptomic analysis on gut samples.
Whereas the host transcriptome was easy, the lack
of a reference genome for my mixed bacterial population is a problem.
Any suggestions how to do the alignment? Has anybody done
metatranscriptomics on Galaxy before?
A recent paper from Leimena et al. (2013, BMC Genomics) claims they
have done the alignment against the complete
NCBI prokaryotic genome database. This sounds like a good solution to
me, but I struggle to get this running.
I am normally on the wet side of the work and my experience with
programming and R is limited.
The aim is to compare the functional capacity of the bacterial
communities in different closely related host species.
Thanks for help,
5130 Comstock Hall
14853 Ithaca, NY
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