Moderator: seidel
seidel ♦ 6.6k
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I work as a scientist at a non-profit research institute.
Posts by seidel
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... One straightforward approach would be to use STAR to generate a count table that you can use with edgeR. Look up the edgeR userguide - it has a rich description of how to quantify differential gene expression given various experimental designs. ...
written 4 days ago by
seidel ♦ 6.6k
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... Excellent! This record has 80 samples so I can just write a loop and parse the results. There are some arguments in your example I didn't know about. Thanks! ...
written 4 days ago by
seidel ♦ 6.6k
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... How does one programmatically get access to all sample information for a given sample using either the GSM number or the SRR number? I've used esearch to get runinfo, and map from GSE series identifiers to GSM sample ids and PRJN SRA identifiers to get corresponding SRR numbers, etc. But for a given ...
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Answer:
A: Perform GO analysis on genome
... I think you mean that you want to assign GO ids to the genes in your genome, as represented by the longest ORF at each locus. Correct? If so, it is common to use homology for the assignments. Find a genome that is closest to your organism - for which GO ids exist, then map your genes to that, and as ...
written 3 months ago by
seidel ♦ 6.6k
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... Have you looked at the affymetrix annotation website https://www.affymetrix.com/analysis/index.affx ? They usually have both a database for looking up annotation for any probe set as well as a download section for downloading files of annotated probes (i.e. which gene /transcript ids match which pro ...
written 9 months ago by
seidel ♦ 6.6k
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Comment:
C: ORFs extractor tool
... Can you give a little more context/information? You mean it finds ORFs in a sequence with a known error? (i.e. it would have to know the ORF sequence in advance) What are you actually trying to accomplish? ...
written 9 months ago by
seidel ♦ 6.6k
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... Your question is far too vague to answer. What is the purpose of your paper? How is what you might be proposing in your paper relevant to the paper you cite? What is the subject of your paper? ...
written 9 months ago by
seidel ♦ 6.6k
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... See the answer to [Question: levels in gene ontology][1] ([https://www.biostars.org/p/237816/#237840][2])
[1]: https://www.biostars.org/p/237816/
[2]: https://www.biostars.org/p/237816/#237840 ...
written 9 months ago by
seidel ♦ 6.6k
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... @noorpratap.singh is telling you to walk through the Seurat tutorial, as it is a good instructional reference/discussion using R on the things you would like to do. ...
written 9 months ago by
seidel ♦ 6.6k
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... It depends on what software you're using, and what you are actually quantifying. Most people gloss over the issue because transcripts and genes are complicated, and specific choices need to be made in order to be precise about either. Nonetheless, generally philosophically speaking: the output of th ...
written 10 months ago by
seidel ♦ 6.6k
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