I have a assembled metagenome and five paired-end metatranscriptomics fastq raw files (all taken with 1 hour in between, so t0, after 1 hour, after 2 hours, after 3 hours and after 4 hours).
Is there a standard workflow to analyze metatranscriptomics data with available metagenomics assembly?
I thought of trimming my reads with trimmomatic, remove rRNA with sortmeRNA and map the reads back on the metagenome assembly. But I have not found any standardized workflow for this. And I am not sure if I should merge the reads before or not.
Also, I would like to obtain a table in the end: sample as the column names and protein names as the row names and tpm values (transcripts per million) in the table.
Does anyone have an idea on how to achieve this? Any help would be highly appreciated. Thank you.