Hello, This metagenomics publication from our team a few years ago took a somewhat similar approach. Perhaps it can be adapted? https://usegalaxy.org/u/aun1/p/windshield-splatter Best, Jen Galaxy team On 10/29/13 8:48 AM, Soren Franzenburg wrote:

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

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Sören Franzenburg

5130 Comstock Hall

Cornell University

14853 Ithaca, NY

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