Pyronoise
We will give it a try.
Thanks
-
Are you doing similarity based clustering to get the haplotypes? Could these singletons be the result of sequencing errors? Perhaps using pyronoise program (http://www.nature.com/nmeth/journal/...meth.1361.html), also available as a part of QIIME (http://qiime.sourceforge.net), could help to reduce this noise?Leave a comment:
-
Singletons -Amplicon sequencing
We performed our first run using 14 MID -14 different specimens per sector with an 4-sector gasket. Under these conditions we are getting ~10,000 reads per specimen. Every seems to be fine with the reads however, we are getting plenty of singletons (40-60%). Thus, if we treat them as 'errors' we would end up with very few haplotypes. We know the complexity (# of haplotypes) is quite high in those samples though, and therefore having so few haplotypes does not make sense. If they are not errors, then their frequency is too low and that does not seem to be correct either. I was wondering what is the 'common' way to define a singleton when dealing with amplicon sequencing? In other words, are they commonly accepted as actual variants or discarded as errors?
XLast edited by Xterra; 06-08-2010, 03:47 AM.
-
Non-coding RNAs (ncRNAs) do not code for proteins but play important roles in numerous cellular processes including gene silencing, developmental pathways, and more. There are numerous types including microRNA (miRNA), long ncRNA (lncRNA), circular RNA (circRNA), and more. In this article, we discuss innovative ncRNA research and explore recent technological advancements that improve the study of ncRNAs.
Nobel Prize for MicroRNA Discovery
This week,...10-07-2024, 08:07 AM -
Metagenomics has improved the way researchers study microorganisms across diverse environments. Historically, studying microorganisms relied on culturing them in the lab, a method that limits the investigation of many species since most are unculturable1. Metagenomics overcomes these issues by allowing the study of microorganisms regardless of their ability to be cultured or the environments they inhabit. Over time, the field has evolved, especially with the advent...09-23-2024, 06:35 AM
Leave a comment: