How to process metatranscriptomics data

Question

[Kumar]

Hi, I have got some samples for metatranscriptomics data analysis.
Please suggest any pipeline and workflow for that.

Thank you, Manoj

[Ram]

What have you tried? What do you plan to achieve with this analysis? That will outline your approach and you can then build a pipeline with that well defined approach in mind.

[seidel]

Please be more specific and descriptive. What do you have? Why do you have it? Where did it come from? (plus what @_r_am said). Your question is similar to "I have some data, please suggest a way to interpret it."

[Kumar]

I would like to compare functional and structural traits of microbial in three different soil samples. I got data from Illumina sequencing of cDNA to study differential expression of carbon genes among three soil samples. Please suggest any pipelines and bioinformatic tools for data analysis. I found some pipelines such as Samsa2 (https://github.com/transcript/samsa2), MetaTrans, please suggest if these are good options.