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If you want to differentiate SNPs/indels from sequencing errors, you should map your reads to the genome/transcript to detect SNPs/indels. Say, using BWA and Samtools. -
Redundancy vs. Artifacts in de novo transcriptomes
Hey all,
I was wondering if anyone knows of (or can think of) a way to assess whether isoforms in a de novo transcriptome assembly are real or an artifact of sequencing/assembly.
I was thinking I might make "unigenes" from my transcripts and then map reads against them. I would then load this data into a genome browser and spot check for low coverage SNPs and insertion/deletions... do you think this would be informative?
Would there be a more high throughput way of doing this than just visually inspecting read alignments?
-Thomas
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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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