Low assignamnet taxa

Hi everyone, currently i have been working with DIAMOND+MEGAN6 pipeline and i think that is the best option for beginners in study of metaganomics. However went i compare my results with other tools like MG-RAST or Kraken2 i see that exist a minor taxon identification with the DIAMOND+MEGAN6 pipeline. I feel some novice in the data analysis but i think that maybe will be related with LCA parameters used in my data. For example MG-RAST bring me around +1000 taxons (genus) identify but went i compare all my samples using MEGAN6 only identify around 300 taxons in all samples

Can you help with that?

Thank you so much for your help

Hi, i want to share that i finaly understand more about megan LCA fuctions. You can change minimun supported percent to 0 for obtain all the taxonomic assignements, however, this value it`s usseful to filter very low read counts (for obtain best assignements). I want to compare with Krarken2 and MG-RAST and i see that for this case maybe its more usseful put this parameter to 0 (default is 0.01). What do you think about that?

Thank you so much for help, I really love use MEGAN6 and for me is the best option to use. Thank for dessing this wonderful software

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Hi there,
my reply here is not related to your question but I hope to get your help.
I could not find this file “megan-map-Jan2021.db.zip” anywhere. May you share me this file to my email?
it is minhtam.smp@gmail.com
Thank you in advance!!

I am sorry to say that our servers are still down and hopefully they will be up again tomorrow.