User: jnf3769

gravatar for jnf3769
jnf376940
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40
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Location:
United States
Last seen:
4 months ago
Joined:
4 years, 3 months ago
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j******@g.rit.edu

Posts by jnf3769

<prev • 23 results • page 1 of 3 • next >
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Phylogram and Ancestral State Reconstruction with known ancestral state
... Howdy Biostars, I was wondering if you all had any program besides BEAST (which I am excluding for pipeline reasons, for now) that allows you to estimate a tree that includes a known ancestral state and a known topology? For instance, a simple 3 taxa example where one taxa (A) is ancestral to the o ...
phylogeny ancestral state reconstruction asr dna written 4 months ago by jnf376940
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DNA Ancestral State Reconstruction in Phangorn (or similiar)
... Howdy Biostars, I have DNA sequence that I have successfully done a bunch of tree building for in BEAST2 to get a time calibrated tree (taxa=8) that answers all the questions I have about topology and branch length. However, I need to know the ancestral states for each bifurcation in the tree. Ther ...
phangorn R phylogenetics ancestral state trees written 7 months ago by jnf376940
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Translocation Calling in human cancer given VCF and BAM files
... Hey Biostars, I am a bit rusty on my genomics tools and was looking for a recommendation for calling translocations in human cancer. I have vcf and bam files (with indecies) that seem to be the result of a few calls to GATK (HaplotypeCaller, IndelRealigner, and BaseRecalibrator). Any suggestions ...
genome cancer translocation variants written 15 months ago by jnf376940 • updated 15 months ago by Kevin Blighe49k
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Comment: C: Quick and Dirty Gene Network
... This is the solution I ended up going with. Thanks! ...
written 16 months ago by jnf376940
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Comment: C: Dose repeatability and reproducibility need to test while validate a fixed bioin
... Izy | You might want to make your question clear. As phrased, your post does not contain a question. I think you are wondering what, after clinically important SNVs are discovered/approved, needs to be done to be sure of an individual's status for that SNV. But I am unsure. ...
written 16 months ago by jnf376940
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Comparative measure of phylogenetic tree resolution
... Hey all, I have a bunch of phylogenetic trees of tissue lineages. I have something on the order of 2000 lineages. For each lineage I have a 100-iteration bootstrap value calculated at every split/node. What I am looking for is a way to get a sense of the overall tree resolution, especially when com ...
phylogeny evolution bootstrap statistics written 16 months ago by jnf376940
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Comment: C: Alignment as BLAST-able database/other alignment avenues
... While I thank you for your response, you again are missing the spirit of the question. The gaps are necessary. It would not be an alignment if I removed the gaps, nor would it inform me to the delineations of the protein sequences in the alignment. ...
written 2.1 years ago by jnf376940
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Comment: C: Alignment as BLAST-able database/other alignment avenues
... Well, that is what I consider the old fashioned way. But in any case, you've completely missed the spirit of my question. Can't make a blast database with an alignment that way--the help flag doesn't specify such a method, at least. https://ibb.co/cSLNKF https://ibb.co/kmcf6v ...
written 2.1 years ago by jnf376940
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Alignment as BLAST-able database/other alignment avenues
... Hey all, I was wondering if there was a way to use an alignment as a local blast database. My problem is as follows: I have an old alignment of concatenated protein sequences that have CHARSET definitions defining the protein beginnings and endings at the bottom of the NEXUS file. Some folks doing ...
alignment nexus blast maftt written 2.1 years ago by jnf376940
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Comment: C: miR KEGG enrichment in Arabidopsis
... I did not need to do alignment or quality control of the sequencing data--it was handed off to me by a legacy researcher and I am more concerned with a qualitative assessment, rather than a quantitative one. I intend to go back and check his work after this to make sure we get the same results, but ...
written 2.6 years ago by jnf376940

Latest awards to jnf3769

Popular Question 15 months ago, created a question with more than 1,000 views. For Coalescent Tree Building
Popular Question 15 months ago, created a question with more than 1,000 views. For Well-resolved Phylogenetic Dataset
Popular Question 15 months ago, created a question with more than 1,000 views. For Generating realistic ABI/AB1 electropherograms for educational purposes
Popular Question 15 months ago, created a question with more than 1,000 views. For OTU distances and assumptions
Scholar 4.0 years ago, created an answer that has been accepted. For A: RNA-seq normalization and differential expression

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