User: Malcolm.Cook

gravatar for Malcolm.Cook
Malcolm.Cook720
Reputation:
720
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Trusted
Location:
kansas, usa
Website:
http://www.google.com/...
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Google Scholar Page
Last seen:
3 days, 21 hours ago
Joined:
7 years, 2 months ago
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m***********@gmail.com

Posts by Malcolm.Cook

<prev • 89 results • page 1 of 9 • next >
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Answer: A: Merge two bigwig(+/- strand) files from RNA-seq
... [WiggleTools](https://github.com/Ensembl/WiggleTools) which provides "Basic operations on the space of numerical functions defined on the genome using lazy evaluators for flexibility and efficiency" should handle this swimmingly ...
written 17 days ago by Malcolm.Cook720
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Comment: C: MISO: Extraction of splicing events from user specified gene annotation (gtf or
... Since that is the documented method for creating MISO compatible annotation, you might consider your problem to be to the yarden's code to work. What did you try? What happened? ...
written 22 days ago by Malcolm.Cook720
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Comment: C: define alternative splice sites
... Actually I don't need the link, as I wrote, "I can not advise you on your use of dexseq for this purpose or interpretation of its output" ...
written 24 days ago by Malcolm.Cook720
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Comment: C: define alternative splice sites
... Hi - Sorry, I can not advise you on your use of dexseq for this purpose or interpretation of its output. (also, your link is to a non-existent page!). Cheers, Malcolm ...
written 24 days ago by Malcolm.Cook720
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Comment: C: Trying to use the gff_to_gtf utiilty in genomeTools
... For another approach to this conversion problem I recommend gffread http://ccb.jhu.edu/software/stringtie/gff.shtml ...
written 27 days ago by Malcolm.Cook720
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Answer: A: define alternative splice sites
... Hi NBS: If you provide * an exhaustive list of the varieties of "exon splicing events" you wish to define * descriptions of what you mean by each * an example or two of each given as a simulated junction.bed file ... then perhaps someone will be able or inclined to take your challenge. In m ...
written 29 days ago by Malcolm.Cook720
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Comment: C: Differential Expression of Splice Junctions using voom-limma/voom-diffSplice
... Hi Stefan, - re 0: thanks for your clarification on the adoption of DEXSeq - re 2-4: do I understand from this that you have 250 individual samples without any biological replicates? If so, this will challenge any differential analysis technique that relies upon variance analysis. However, y ...
written 5 weeks ago by Malcolm.Cook720
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Answer: A: Differential Expression of Splice Junctions using voom-limma/voom-diffSplice
... Please explain more carefully your experiment and the questions you want to put to your data. I ask because I expect you are really interested in the "expression of splice junctions" as compared to something else (say, roughly, "expression of exons". ) I guess this because you are considering DEXS ...
written 6 weeks ago by Malcolm.Cook720
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Comment: C: Cuffdiff promoter.diff is empty
... can you provide the content of contrasts.txt? ...
written 11 weeks ago by Malcolm.Cook720
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Comment: C: cuffdiff vs cuffnorm vs cuffquant
... Hi Devon, What in you view is contemporary update on cuffdiff's [Differential splicing tests][1] [1]: http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/#differential-splicing-tests---splicingdiff or does that still count as a "good reason" Thx! ...
written 3 months ago by Malcolm.Cook720

Latest awards to Malcolm.Cook

Scholar 6 months ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Demultiplex Illumina With Barcodes On Identifier Line
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Demultiplex Illumina With Barcodes On Identifier Line
Scholar 16 months ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Good Answer 2.1 years ago, created an answer that was upvoted at least 5 times. For A: Extract Cds Fastas From A Gff Annotation + Reference Sequence
Scholar 2.5 years ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Demultiplex Illumina With Barcodes On Identifier Line
Scholar 3.0 years ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Extract Cds Fastas From A Gff Annotation + Reference Sequence
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Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Extract Cds Fastas From A Gff Annotation + Reference Sequence
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Demultiplex Illumina With Barcodes On Identifier Line
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Which Are The Best Collections Of Bioinformatics Tools For Ngs Analysis And Sequ
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: How To Visualize Spliced Alignments Of Next Gen Sequencing Data?
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Quick Programming Challenge: How Do I Calculate Reference Coverage From A Table

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