Moderator: Alex Paciorkowski

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Rochester, NY USA
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Our group studies disorders of human brain development.

Posts by Alex Paciorkowski

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Comment: C: Large File Transfers Of Ngs Data: Rsync / Bbcp / Unison / What?
... I'd try having a direct conversation with Globus support about your exact requirements, if you haven't already done so. There may have been some changes since this answer was posted ~2 years ago. Globus ought to be ideal for the kind of transfers you mention. Usually they will work directly with you ...
written 2.3 years ago by Alex Paciorkowski3.3k
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Answer: A: Mapping Variants to Protein Seqeunces
... This may be similar to https://www.biostars.org/p/51204/ and also https://www.biostars.org/p/119241/#119985 It sounds like you need to further annotate your variants. There are many such tools. Try the links above, and try these: Ensembl's variant effect predictor: http://useast.ensembl.org/info/d ...
written 2.7 years ago by Alex Paciorkowski3.3k
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Answer: A: what is your daily must see bioinformatics web site?
... Biostars and Biostars/Planet, of course. ...
written 3.0 years ago by Alex Paciorkowski3.3k
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Answer: A: Help with Creating Gene Diagram for Research Article
... For the location of the mutations in the gene, a combination of Scrible, fancyGene, or maybe GSDS should get you there. If you have knowledge or interest in R, some of the image can probably be generated using genoPlotR. To be honest, I bet most people would draw something like this out in Adobe Pho ...
written 3.0 years ago by Alex Paciorkowski3.3k
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Comment: C: Why are we still using Bam files? And not Cram, HDF5 or improved Bam files?
... And those running labs would ask who is going to pay for such a warehouse. ...
written 3.0 years ago by Alex Paciorkowski3.3k
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Comment: C: Does CNVs are genetically inherited?
... A couple of inaccurate things in your post @Kizuna: 1) A CNV shared between 50 subjects (with the same disease) could very well be disease causing. This happens all the time. Deletion 22q11 syndrome. Williams syndrome. The list is very long of examples in human genetic disease. 2) I'm not sure wha ...
written 3.0 years ago by Alex Paciorkowski3.3k
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Comment: C: Regarding GATK pipelie
... This is a question, not a tutorial. Also, there are many GATK-related answers here, all findable by search. For example: https://www.biostars.org/p/57238/#57240 https://www.biostars.org/p/56563/#56578 ...
written 3.1 years ago by Alex Paciorkowski3.3k
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Comment: C: Web server to analyze sequence data
... I can't answer most of your questions because I have no idea what some of your parameters are. When you say "the web app works fine with a small # of sequences" -- what number is small? "Large sequence files" - what number is large? What exactly do you mean by "it crashes" -- do you get an out of me ...
written 3.1 years ago by Alex Paciorkowski3.3k
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Comment: C: Laboratoy Scientific - Biochemist
... How did you measure your zygosity on your Sanger read? You probably have preferential amplification of one allele over the other. Do you see the mutation in your chromatographs? Have you done bidirectional sequencing? If it's visible on the chromatographs on bidirectional Sanger sequencing, I wouldn ...
written 3.1 years ago by Alex Paciorkowski3.3k
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Comment: C: CHI SQUARE TEST IN R for SPNs bacterial data
... So you want to evaluate for the association of each SNP with drug resistance or sensitivity? What is your null hypothesis? That a given SNP is not associated with resistance? I think you need to be still more detailed. Is your question about chi-squared and how to frame your hypothesis, organize you ...
written 3.1 years ago by Alex Paciorkowski3.3k

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