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
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
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!!