billytaj
commented
1 year ago Any non-relevant material that can be removed from your dataset will ultimately speed up your analysis as the pipeline won't be bogged-down by junk data. If your analysis ends up being heavily biased towards non-bacterial organism, then the result is still valid, but the data is unclean and results in wasted compute cycles.
MetaPro does not filter or remove poly-A tails. It is assumed that the user will have done that outside of the pipeline.
Hi, Found this pipeline after watching the metatranscriptomic workshop on bioinformatics.ca's channel.
Apologies if the question is not relevant or link to the software. I have a question regarding metatranscriptome sample preparation.
If i plan do a metatranscriptome sample of rice, it is suggested for me to deplete the polyA tailmaterial in the total RNA or its okay just to sequence the mRNA without having to enrich the bacterial transcript. I am just worried the dominance of the host reads will reduce the signal of the bacterial mRNA.
if no polyA tail depletion is not necessary, whats is the raw reads that is considered enough? is 20 million reads is okay?