Hi everybody, 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, Sören
--------------------------------------------- Sören Franzenburg 5130 Comstock Hall Cornell University 14853 Ithaca, NY