Tweet
What conditions do I use to anneal the adapters and what concentration is optimal for ligation of adapters to the fragmented genomic DNA.
-
-
What kind of experiement are you doing? de novo sequencing, exome capture, etc? you can find these information in a standard protocol ...Nicolas Tremblay
Graduate Student
Cardiovascular Genetics - Andelfinger Lab
CHU Ste-Justine Research Center -
I mapped the illumina reads (unpaired reads) using Bowtie2. Now i want to extract the uniquely mapped reads. the formate of mapping summary is...
20000 reads; of these:
20000 (100.00%) were unpaired; of these:
1247 (6.24%) aligned 0 times
18739 (93.69%) aligned exactly 1 time
14 (0.07%) aligned >1 times
93.77% overall alignment rate
So please help me if anyone know that how to extract the uniquely mapped reads..Comment
-
It depends on what metrics you want to use to call something uniquely mapped. It's more useful to think of alignments in terms of probability of being correct, which which case just use something like MAPQ>=10. BTW, bowtie2 will give multimappers MAPQ scores of 0 or 1, but that doesn't mean that alignments with MAPQ scores of 2 are that reliable.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...04-22-2024, 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