Hello All
I am doing a 16S metagemomic (Illumina Miseq) pipeline (mostly with Qiime) on a virtual machine (all installed all running) and I was testing together with a coworker using the exact same pipeline and same sample and in the end we got different Taxonomic results.
We checked step by step to see where we diverged and we realized its when we cluster to OTU assignment. We start this with a fasta file with all the reads (we have the same number) and then after OTU picking we are very different. Specially strange since I get no Unidentified bacteria (basically impossible in my opinion) and he gets a decent % of those for the exact same sample.
For OTU picking we used pick_otus.py and I am attaching the complete log file. What can happen during this to end up in a different final result of the exact same sample?
I deeply appreciate any feedback on this please!
Thank you so much!
Ana
I am doing a 16S metagemomic (Illumina Miseq) pipeline (mostly with Qiime) on a virtual machine (all installed all running) and I was testing together with a coworker using the exact same pipeline and same sample and in the end we got different Taxonomic results.
We checked step by step to see where we diverged and we realized its when we cluster to OTU assignment. We start this with a fasta file with all the reads (we have the same number) and then after OTU picking we are very different. Specially strange since I get no Unidentified bacteria (basically impossible in my opinion) and he gets a decent % of those for the exact same sample.
For OTU picking we used pick_otus.py and I am attaching the complete log file. What can happen during this to end up in a different final result of the exact same sample?
I deeply appreciate any feedback on this please!
Thank you so much!
Ana