Moderator: seidel

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seidel6.6k
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I work as a scientist at a non-profit research institute.

Posts by seidel

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Comment: C: RNA-Seq Differential gene expression
... 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 seidel6.6k
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Comment: C: Programmatic access to Sample Information from GEO via GSM or SRR number
... 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 seidel6.6k
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Programmatic access to Sample Information from GEO via GSM or SRR number
... 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 ...
geo written 4 days ago by seidel6.6k • updated 4 days ago by vkkodali850
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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 seidel6.6k
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Comment: C: Affymetrix Soybean Gene 1.1 ST Array PROBES IDs to Ensembl transcripts IDs
... 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 seidel6.6k
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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 seidel6.6k
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Comment: C: Comparing work done on RNA seq data
... 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 seidel6.6k
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Comment: C: What is the meaning of the level in groupGO Clusterprofiler ?
... 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 seidel6.6k
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Comment: C: single cell RNAseq: From counts or RPKM > PCA > tSNE visualization of PCA
... @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 seidel6.6k
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Answer: A: What is the difference between gene FPKM and transcript FPKM values?
... 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 seidel6.6k

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Popular Question 9 months ago, created a question with more than 1,000 views. For Archiving BAM files and analysis
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Technical Or Biological Replicate
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Commentator 10 months ago, created a comment with at least 3 up-votes. For C: Experimental Techniques To Measure Protein-Protein And Protein-Ligand Structure
Scholar 16 months ago, created an answer that has been accepted. For A: genomicranges outside sequence bounds
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