Question: Bacterial Metatranscriptomes
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Soren Franzenburg • 10 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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modified 5.1 years ago
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Jennifer Hillman Jackson ♦ 25k
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written
5.1 years ago by
Soren Franzenburg • 10
