Entering edit mode
3.3 years ago
bioAddict
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0
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.
In general is a good idea to merge after mapping.
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.
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.
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?