Hi everyone. I am using deconseq to remove human, bacterial, viral and archaeal contaminant reads from a bivalve RNAseq dataset (HISEQ 2x300bp), and I would like to use this tool to remove any potential phytoplanctonic contaminants as well. Are there any existing database that would fit the bill? Thanks in advance for your feedback.
Thank you for your reply, Artur. I actually do not know whether phytoplanctonic contaminants will be prevalent or not. Looking at the literature on bivalve transcriptomes using tissues that could be contaminated with, say, microalgae or diatoms, either people keep individuals in controlled conditions to avoid the co-extraction of foreign RNA, or they do not address the issue of contamination.
kindly see database info in our portal biocuration and check in genome solution page with your search queries www.biocurationssl.com
yes - I started implementing this approach using the SILVA database. thanks!
- Badges
- Science method
- Similar topics
- Biological Science
- Ecology