User: eric.kern13
eric.kern13 • 120
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Posts by eric.kern13
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... Your link currently gives this thread as the first hit. Profit indeed. ...
written 25 days ago by
eric.kern13 • 120
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... Using the ncbi UNIVEC reference or similar, you can do a BLAST search against common artificial sequences.
https://www.ncbi.nlm.nih.gov/tools/vecscreen/univec/ ...
written 3 months ago by
eric.kern13 • 120
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... What have you tried so far? One sensible solution might be to try:
- whatever you would try if you didn't have to worry about low counts; maybe K-means
- some out-of-the-box method such as PAGODA. http://hms-dbmi.github.io/scde/pagoda.html
If those don't get you to where you need to be, then where ...
written 9 months ago by
eric.kern13 • 120
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Comment:
C: Question about dbSNP rs #s
... Do you know of an easy way to update rsid's that have been retired? ...
written 12 months ago by
eric.kern13 • 120
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... (I would like to hear the answer to this as well.) ...
written 15 months ago by
eric.kern13 • 120
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... This is an interesting comment and I'd like to understand it better. Are you using the word "regularization" in the statistical sense, for example as in "Tikhonov regularization"? If so, can you describe the statistical methods you have in mind? Also, how do you know that there are more duplicates p ...
written 15 months ago by
eric.kern13 • 120
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... Suppose I have the following read:
AAGGAAGGAAGGAAGGACTTCCTT
I want to align it to one of these two reference sequences:
AAGGAAGGAAGGAAGGACAAGGAA
AAGGAAGGAAGGAAGGCCTTCCTT
Clearly, the second reference sequence is where the read belongs: there's only one mismatch. The maximum mappable ...
written 17 months ago by
eric.kern13 • 120
• updated
17 months ago by
Santosh Anand • 4.1k
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... Works like a charm. Thank you very much! ...
written 18 months ago by
eric.kern13 • 120
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... I tried to; it didn't work. I'll try again. ...
written 18 months ago by
eric.kern13 • 120
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... I want to retrieve all genes corresponding to a given mammalian phenotype ontology term (for example, MP:0005375), preferably within R. Are there tools to do this? Can I do it within BioMart? Or is the best bet to build something around the APIs [here][1] or [here][2]?
Related: [similar question fo ...
written 18 months ago by
eric.kern13 • 120
• updated
18 months ago by
Mike Smith • 890
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For 1000 genomes technical data: match exon capture probes to samples
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For Read depths from 1000G exome sequencing are almost all zero.
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For +/- strand conventions for probe sequences
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