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
Sören Franzenburg
5130 Comstock Hall
Cornell University
14853 Ithaca, NY
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