Moderator: igor

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igor11k
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Posts by igor

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Comment: C: Somatic SNVs vs. Germline SNPs for allele-specific copy number analysis
... With germline, you know the original frequency is either 50% or 100%. With somatic, you do not. As you said, somatic variants are still informative. They can be used to estimate tumor purity and clonality, and there are specialized tools for that. ...
written 7 weeks ago by igor11k
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Comment: C: How is 1000 genomes so accessible when many other genotype/sequencing projects a
... I believe genetic data is considered PHI in the US ([source][1]). Of course, that would not matter if the participants give consent to release it. [1]: https://www.hhs.gov/hipaa/for-professionals/special-topics/genetic-information/index.html ...
written 7 weeks ago by igor11k
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Comment: C: Somatic SNVs vs. Germline SNPs for allele-specific copy number analysis
... > is there anything wrong with using somatic SNVs as well? There will be a lot less of them, so the impact will be negligible. ...
written 7 weeks ago by igor11k
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Comment: C: Negative values HTSeq2
... You may want to go through a basic R tutorial. If you plan on using DESeq2, you'll need to know some basics like what the different data types are and how to read/write files. ...
written 7 weeks ago by igor11k
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Comment: C: Does GATK provide datasets to test their pipelines? (Learning purpose)
... Some of them are from 2020 (use the directory name, not the modified date to gauge the age). I assume various events stopped in March due to the pandemic. GATK4 has been out for over 2 years and most of the tools have not changed much. ...
written 7 weeks ago by igor11k
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Comment: C: Does GATK provide datasets to test their pipelines? (Learning purpose)
... You can also check their workshops which have a lot of info and examples: https://drive.google.com/drive/folders/1y7q0gJ-ohNDhKG85UTRTwW1Jkq4HJ5M3?usp=sharing ...
written 7 weeks ago by igor11k
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Comment: C: Does GATK provide datasets to test their pipelines? (Learning purpose)
... Why do they include RNA-seq Cell Ranger data? That does not seem GATK-related. ...
written 7 weeks ago by igor11k
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Answer: A: Applying batch correction to single-cell RNA-seq in diffferent time points
... > if you are to use batch correction you should have biological or technical batches from the "same condition" From the [integration vignette][1]: "These methods aim to identify shared cell states that are present across different datasets, even if they were collected from different individuals, ...
written 7 weeks ago by igor11k
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Comment: C: How to write a literature review article in bioinformatics?
... > If you're asking how to write a review, then you likely have no business writing one You could still try to learn how the process works to be better prepared in the future. Have to start somewhere. ...
written 8 weeks ago by igor11k
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Comment: C: all coding regions .bed file hg38 Whole Genome Sequencing
... Don't the `exon` entries contain non-coding UTRs? ...
written 8 weeks ago by igor11k

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