This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Humann2 for metatranscriptomic data

I have some metatranscriptomic data from a community consisting of one green alga and a mixed population of bacteria. I want to annotate the transcripts from both eukaryotic and prokaryotic community members and get pathway abundance measures so that I can compare the metabolic activities between two different treatments. The Humann2 software provides an excellent pipeline for the prokaryotic portion of my data but excludes eukaryotes. I know that you can provide custom databases to Humann2. Does anybody have an idea of a suitable eukaryotic database to format for this purpose and if this approach would work to get me a comprehensive analysis of the whole community transcript pool?

rna-seq metatranscriptomics humann2
• 2,638 views • link
written by cook284 • cook284

According to the documents of HUMAnN2: MetaPhlAn2 and ChocoPhlAn pangenome database are used to facilitate fast, accurate, and organism-specific functional profiling, Organisms included are Archaea, Bacteria, Eukaryotes, and Viruses. It looks like the Eukaryotes genome has been included.

• 0 views • link
written by Shicheng Guo Shicheng Guo

0 answers

No answers yet.

Log in to answer this question.

More posts like this