You can also use CNVrd2:
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THetA2 can infer absolute copy number from read depth: http://compbio.cs.brown.edu/projects/theta/
It runs using the segmentation output of BIC-seq, ExomeCNV, EXCAVATOR or CNVkit, and infers the tumor cell purity, subclone composition if present, and absolute copy number of each segment.Leave a comment:
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Inferring absolute copy number by using NGS data
Hi all,
I have a set of CNV loci called from NGS data, and now I want to do genotyping, i.e. inferring the absolute copy number from this dataset. To my knowledge CopySeq can do this work, but unfortunately I cannot run CopySeq successfully. Does anyone know how to run CopySeq or is there any other read-depth-based software that can do the same work?
Thanks in advance..
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The field of immunogenetics explores how genetic variations influence immune responses and susceptibility to disease. In a recent SEQanswers webinar, Oscar Rodriguez, Ph.D., Postdoctoral Researcher at the University of Louisville, and Ruben Martínez Barricarte, Ph.D., Assistant Professor of Medicine at Vanderbilt University, shared recent advancements in immunogenetics. This article discusses their research on genetic variation in antibody loci, antibody production processes,...11-06-2024, 07:24 PM -
Next-generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR) are essential techniques for investigating the genome, transcriptome, and epigenome. In many cases, choosing the appropriate technique is straightforward, but in others, it can be more challenging to determine the most effective option. A simple distinction is that smaller, more focused projects are typically better suited for qPCR, while larger, more complex datasets benefit from NGS. However,...10-18-2024, 07:11 AM
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