Assembly of three biological replicated metagenomics data

Question

[bioAddict]

Hi there,

I am currently performing a metagenomic analysis on transcriptomics data. But I'm not sure what strategy to adopt in relation to the assembly.

In fact, the transcriptomics data are from three biological replicates per sample. I am wondering whether I should concatenate the replicates during assembly or not.

And what would be the impact if I wanted to analyse my results with EdgeR. As a newbie in bioinformatics, your help would be appreciated.

[Lila M]

In general is a good idea to merge after mapping.

• You should perform your QC with separate files, to check for possible batch effects, and merge after being sure no batch effects are present.
• mapping files in parallel is faster than mapping one large size

[bioAddict]

It seems like you didn't get what I was explaining. In fact, for the metagenomics study, I extracted the unmapped reads from the transcriptomics data to separate the host transcriptomics from microbiota transcriptomics.

Since I'm in search of RNA virus, I want to perform an assembly on the unmapped reads. That's why I'm wondering whether I need to concatenate the unmapped reads of the three biological replicate before performing the assembly.

And I need to understand whether the concatenation of the replicate might be useful of the statistical analysis or not if I will use EdgeR.

[andres.firrincieli]

Hi bioAddict,

If you are in search of something that usually have a very low coverage, concatenating the reads would greatly increase the chances of getting what are you looking for.

And I need to understand whether the concatenation of the replicate might be useful of the statistical analysis or not if I will use EdgeR.

Once you have assembled the meta-transcriptome, you can use that as reference for transcript quantification by mapping back reads from each sample.

The real question is: Does edgeR works for metagenomic/metatranscriptomic data?