Tweet
We have data of yeast (Yarrowia)sequenced using Illumina paired-end. Each read R1 and R2 has ~41 million reads. Read length is 150 and insert size is 300. I have used velvet for de novo assembly. The highest value of N50: 22726 was obtained for Kmer 93. Total contigs are ~1900. Scaffolding was done using Contiguator. Gapfiller was used to fill the gaps. Closest Yarrowia homolog has a length of ~ 20MB. Using our data I got after gapfilling ~17MB. How to fill the gap of 3MB ? Eagerly awaiting your inputs
-
-
I suggest you try assembling with Spades; it often yields better continuity than Velvet. -
Why do you expect the genomes to have the exact same sizes? "Closest" sequenced homolog can still be far far away. I would say you go for more meaningful assembly quality assessment criteria.
Alternatively, you could just randomly try assemblers until you find one that gives you ~20MB
Comment
-
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 on Modified Bases...Yesterday, 07:01 AM -
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...04-04-2024, 04:25 PM
Comment