Tweet
They give you a pipeline on the website as well as the command line options. It should be just as easy as using samtools in order to call snps, am I right or am I wrong? Why or why not?
-
-
mate check out the youtube videos on the GATK package .. its not as simple as just using samtools to call out snps because INDELs and systematic biases affect the calls ... samtools does not adjust for these..... spend the time and learn the GATK package, its well worth it -
The GATK is very picky about the formatting of its input files making it much more difficult to use the the samtools pipeline. The formatting is important though because the pipeline generally makes use of all available relevant information making it more sensitive than samtools.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