Moderator: karl.stamm

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karl.stamm3.6k
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Posts by karl.stamm

<prev • 475 results • page 1 of 48 • next >
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Comment: C: Fisher strand (FS) 0?
... p-values are not effect sizes. Anything p>0.2 is equivalent to saying 'no evidence' you shouldn't judge the difference between a p=0.5 and a p=0.9 to mean anything at all. They tend to get conflated with strength of association, because in introductory statistics they may appear to be correlated, ...
written 12 days ago by karl.stamm3.6k
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Comment: C: Fisher strand (FS) 0?
... This one https://gatkforums.broadinstitute.org/gatk/discussion/6724/question-for-fisherstrand seems to say that high FS indicates strand bias, and possibly false positives from low coverage regions. Makes sense that a position with "25,19:17,12" has really 0 apparent strand bias. ...
written 12 days ago by karl.stamm3.6k
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Comment: C: Fisher strand (FS) 0?
... What tool generated this data? Including the command line can be helpful too. From what I can interpret of the data you posted originally, it looks like quite a normal HET, with basically balanced reads. What did you expect of the FS field? ...
written 12 days ago by karl.stamm3.6k
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Comment: C: Should I Run Clustering on PCA or t-SNE Components?
... and dont forget to look at PCA dimensions 3&4, there's so much beyond dimensions 1&2. ...
written 6 weeks ago by karl.stamm3.6k
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Comment: C: Should I Run Clustering on PCA or t-SNE Components?
... Plain PCA on the whole dataset gives the broadest picture. it is vulnerable to scaling problems: if there are two major clusters very distinct, like dead cell / alive cell, you wont be able to see nuanced differences in alive cell type A vs B. That's where a rescaler like tSNE or UMAP can be helpfu ...
written 6 weeks ago by karl.stamm3.6k
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Answer: A: Should I Run Clustering on PCA or t-SNE Components?
... Why are you trying to cluster the data? Your goals will direct the best method. Initially I'd agree with what you've found already: tSNE and UMAP are for visualization and will manipulate the sample-to-sample distances. Clustering done after that will be biased and give you something easy you can ...
written 6 weeks ago by karl.stamm3.6k
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Comment: C: Why does ExpansionHunter ignore unmapped reads?
... What was the sequencing technique? I've seen coverage humps like that when using Whole Exome kits. It's not intended to capture broad sections of genome. There may be other areas with similar sequence motif that are 'stealing' your reads, since this one only has 60bp (20x3) and you may have 100bp r ...
written 9 weeks ago by karl.stamm3.6k
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Comment: C: Why does ExpansionHunter ignore unmapped reads?
... If the reference has a region of sufficient motif, then your reads will align to it. Maybe you end up with very high coverage of the tandem repeat segment. In my experience the unmapped reads tend to be technical artifacts or low quality data. ...
written 9 weeks ago by karl.stamm3.6k
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Comment: C: Needleman-Wunsch with Python
... https://www.biostars.org/p/75548/ ...
written 12 weeks ago by karl.stamm3.6k
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Comment: C: str handling in python
... So don't use a language you aren't familiar with. If you have no programming skills, try the programming forums. It's not a bioinformatics issue. ...
written 3 months ago by karl.stamm3.6k

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Scholar 10 weeks ago, created an answer that has been accepted. For A: multithreading in psiblast
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