User: btsui

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btsui290
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Posts by btsui

<prev • 35 results • page 2 of 4 • next >
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Answer: A: Allele counting tool for a list of known indels from paired end sequencing data
... bam-readcount: https://github.com/genome/bam-readcount ...
written 22 months ago by btsui290
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Comment: C: TCGA expression data (TPM)
... TPM and RPKM/FPKM are highly correlated at gene level quantification. TPM use transcript length to normalize. FPKM use gene length to normalize. And the transcript length is highly correlated with gene length. My take is that both TPM and RPKM/FPKM are reasonable estimates for expression levels, my ...
written 22 months ago by btsui290
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Comment: C: how to detect mutation from viral RNA-seq data
... My understanding is that TCGA was able to use RNA-seq to detect HPV infection in their papers (most likely in head and neck cancer paper), so I guess it is possible to detect viral genome from the RNAseq. If the NDV genome is very conserved, you might as well first align it to the NCBI viral refere ...
written 22 months ago by btsui290
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Comment: C: Probabilistic PCA on very sparse SNP matrix
... Can you first filter the sites that always have missing values first? ...
written 22 months ago by btsui290
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Answer: A: Grail: reflow on AWS vs others (snakemake/cfncluster, etc)
... There is AWS batch (https://aws.amazon.com/batch/) for submitting jobs. ...
written 22 months ago by btsui290
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Comment: C: TACC vs SDSC vs HTCondor
... Also, buying in and opting out with AWS is way simpler. **You can do it online**. All you need is a credit card to try out AWS. The computing centers you mentioned sounds like the ones where you have to communicate back and forth through email. ...
written 22 months ago by btsui290
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Comment: C: TACC vs SDSC vs HTCondor
... I used SDSC before. Buying the machines on SDSC isn't cheap, it's like $10k per node, but they do offer a good ideal on storage called universal storage which costs roughly $1000 per month for a minimum of 200TB. But yeah, for hosting private nodes in SDSC you have to beware of the extra cost of mai ...
written 22 months ago by btsui290
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Blog: Buying computing infrastructure vs adopting the Cloud in Bioinformatics
... The recurrent question in data-intensive bioinformatics labs often revolves around which computing infrastructure to use. In the past four years as a bioinformatics Ph.D. student, I have both received and offered solicited and unsolicited advice regarding computing infrastructures using my prior exp ...
sequence blog written 22 months ago by btsui290
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Comment: C: How to detect segmental duplications?
... My guess is that you still need to find the synteny block mapping between your case and control groups first. If you don't see a coverage difference at all in any of the synteny blocks between case and control, you might want to reevaluate your endeavour.... I could be wrong, but my understanding i ...
written 22 months ago by btsui290
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Comment: C: Best technique for CNV and mutation analysis
... For accurate CNV counting, my understanding is that you can design probes to target those two genes and then use ddPCR for quantification. Are you targetting for specific mutations? You might want to read this paper (http://science.sciencemag.org/content/early/2018/01/17/science.aar3247). ...
written 22 months ago by btsui290

Latest awards to btsui

Scholar 23 months ago, created an answer that has been accepted. For A: Assembly of wheat genome
Scholar 23 months ago, created an answer that has been accepted. For A: Assembly of wheat genome

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