User: eric.kern13

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eric.kern13100
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Posts by eric.kern13

<prev • 36 results • page 1 of 4 • next >
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Answer: A: Adapter/Linker/Primer Sequence Database?
... 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 21 days ago by eric.kern13100
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Answer: A: Overdispersion for single cell RNA seq experiments
... 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 6 months ago by eric.kern13100
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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 9 months ago by eric.kern13100
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Comment: C: Duplicated Reads In Rna-Seq Experiment
... (I would like to hear the answer to this as well.) ...
written 12 months ago by eric.kern13100
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Comment: C: Should We Remove Duplicated Reads In Rna-Seq ?
... 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 12 months ago by eric.kern13100
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What happens during seed stitching when STAR initially gets the wrong MMP?
... 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 ...
star rna-seq written 14 months ago by eric.kern13100 • updated 14 months ago by Santosh Anand3.8k
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Comment: C: Retrieve all genes under a mammalian phenotype ontology term
... Works like a charm. Thank you very much! ...
written 15 months ago by eric.kern13100
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Comment: C: Retrieve all genes under a mammalian phenotype ontology term
... I tried to; it didn't work. I'll try again. ...
written 15 months ago by eric.kern13100
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Retrieve all genes under a mammalian phenotype ontology term
... 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 ...
R biomart go mammalian phenotype ontology written 15 months ago by eric.kern13100 • updated 15 months ago by Mike Smith820
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Comment: C: cell surface receptor genes
... Thanks for this list of resources! ...
written 22 months ago by eric.kern13100

Latest awards to eric.kern13

Popular Question 21 days ago, created a question with more than 1,000 views. For Mappability Scores from bigWigAverageOverBed all zero
Popular Question 4 months ago, created a question with more than 1,000 views. For +/- strand conventions for probe sequences
Popular Question 6 months ago, created a question with more than 1,000 views. For Pysam cannot find index
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Popular Question 22 months ago, created a question with more than 1,000 views. For Pysam cannot find index
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