User: Denis

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Denis110
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Posts by Denis

<prev • 79 results • page 2 of 8 • next >
7
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Bootstrap values on the phylogenetic tree in Ape r package
... Hi there, I've constructed the tree with bootstrap supports in `Ape` package. But i'd prefer to get bootstrap values in percentage not in absolute number of replications. How can i do that in `Ape`? ...
R phylogenetics written 8 weeks ago by Denis110
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Comment: C: How to Calculate FDR in permutation F test
... Hi! Did you find answers for the questions you asked? To my understanding for each gene you have to calculate: perm_p-value= number of p-values<=p-value experimental +1/total number of permiutations+1. So your formula is not correct in this way. To perform `FDR` correction you should take your ra ...
written 8 weeks ago by Denis110
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Comment: C: Performing fast bootstrap in R using ape package
... How many samples you have? I do almost the same thing in `Phangorn package` with 13 samples and 7.5K of `SNPs`. So it took just 1-2 minutes for 2000 `bootstrap` replics. ...
written 8 weeks ago by Denis110
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Comment: C: Calculate distance matrix from nucleotide alignment with multiple IUPAC ambiguit
... Thanks! As i understand `F81 model` is four parametric in typical case. I'm wondering if it would have much more parameters in case of `IUPAC ambiguity` characters? It will extract the base frequences from the nucleotide alignment, which i'm using as input. Am i right? ...
written 8 weeks ago by Denis110
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Comment: C: DESeq2 modelling and Wald's test
... Sorry, but it's stiil not quite clear for me. I thought that `T-test` for two (in majority experiments) independent groups would be more intuitive and obvious. So, why a single group `T-test`? In addition, when i perform `T-test` for example in `R` i don't need anything except trait observations in ...
written 9 weeks ago by Denis110
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Comment: C: DESeq2 modelling and Wald's test
... Kevin, thanks for your explanation. Let me one naive question please? Why we need to make a `GLM` model before performing a `Wald test` itself (as i can understand it's just a simple `t-test` in rough approximation?)? Why not just perform a `Wald test` on count data? ...
written 9 weeks ago by Denis110
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Comment: C: Unexpected Bowtie2 behavior with --phred64 and --phred33 flags
... Hi Devon Ryan! Many thanks for your reply, it makes things clear. Let me ask just one more question please? I'm wondering how single mismatch with quality "f" (`ASCII` 102) will be scored in `Phred+33` mode? ...
written 12 weeks ago by Denis110
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Unexpected Bowtie2 behavior with --phred64 and --phred33 flags
... I'm stiil not able to figure out how `Bowtie2` deal with different `Phred quality` encoding. In my recent post: [enter link description here][1] [1]: https://www.biostars.org/p/381067/ genomax pointed me to use `--phred64` flag when using `Bowtie2` to map `Phred+64` encoded reads. I tried both ...
software error alignment written 12 weeks ago by Denis110 • updated 12 weeks ago by Devon Ryan91k
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Comment: C: Mapping Phred+64 encoded reads with Bowtie2
... Thanks! But why i didn't get error by using this command line? I use this command a long time and only recently realized that the reads have `Phred+64 encoding`. How it may influence on the mapping results (everything looked well in resulted `SAM` file i usually got)? ...
written 12 weeks ago by Denis110
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Mapping Phred+64 encoded reads with Bowtie2
... Hi, I faced with strange behavior of `Bowtie2`. I mapped reads with `Phred+64` encoding by command: bowtie2 --very-sensitive -x index -U R1.fastq -S Alignment.sam I'm wondering why i didn't get any error message in that case? Is `Bowtie2` able to determine reads encoding format automatically ...
genome software error alignment written 12 weeks ago by Denis110 • updated 26 days ago by Biostar ♦♦ 20

Latest awards to Denis

Scholar 7 weeks ago, created an answer that has been accepted. For A: Bootstrap values on the phylogenetic tree in Ape r package
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Bootstrap values on the phylogenetic tree in Ape r package
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Demultiplexing of the Illumina PE data
Supporter 13 months ago, voted at least 25 times.

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