Tweet
I've just finished my first shot at assembling a metagenome sample derived from a marine environment using Velvet, VelvetOptimizer and Metavelvet. Running the assembly with the recommendations from VelvetOptimizer (kmer size of 31), I was getting very short contigs ~100-400 bp. Increasing the kmer size beyond this to 37 resulted in longer contigs 100-3K. When I started analyzing the coverage and reads for several contigs, I noticed that some short contigs i.e. 90bp had about 10K reads and a coverage of 20X for example. Some of the longer contigs 1K or 2K had less reads (200) and lower coverage. My question is if there are certain steps I can take now to filter out contigs that might not be useful in the annotation step for example, or that could be chimeric? I'm not sure how to further proceed. Before I try using a different assembler I'd like to understand how these results could be further analyzed before proceeding to the annotation step.
-
The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...05-06-2024, 07:48 AM -
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...04-22-2024, 07:01 AM
Comment