How to perform the anaysis of taxonomic on raw reads from the mixed sample

[jennaj]

Hi @ps2pspgood

@ps2pspgood

I found the tutorial: " 16S Microbial Analysis with mothur" however, I tried with the current data of NGS data on insects, it took so much time on making contigs of non bacterial reads. I am wandering if there is any methods that can get rid of reads that is non bacterial in the first hand.

The samples are mixed so all of that would happen at the same time, correct? Or am I not understanding correctly?

Are the jobs just taking a long time to process? If they failing because of this at one server you could try at a different server that offers longer runtimes, UseGalaxy.eu is one choice.

The parts where you are making the contigs is what will allow you to find all the reads that may belog to species that you are not interested in. A regular pipeline where you would map to filter out probably wouldn’t work for this step, or not that I know of. You could check literature sources for alternative ideas though.

@ps2pspgood

Currently, I can use Kraken2 to perform the analysis. However, I have following few questions.

1. How can I focus only on the bacteria and remove the rest of data and make a summary table or visualization (the percentage of each bacteria strain).

For this, you could filter the Kraken2 results before the visualization steps.

You could do this directly on the output report with data manipulation tools, or use a tool like this to filter the entire read dataset Krakentools: Extract Kraken Reads By ID Extract reads that were classified by the Kraken family at specified taxonomic IDs

Hope this helps but you can ask more questions!