User: User000

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User000270
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Posts by User000

<prev • 186 results • page 2 of 19 • next >
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Comment: C: Performing fast bootstrap in R using ape package
... yeah, it says Running parallel bootstraps... and also is using 6 cores... Do you think it is enough for 5000 snps and something is going wrong? ...
written 14 months ago by User000270
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Performing fast bootstrap in R using ape package
... Dear all, I would like to perform a nj tree with 1000 bootstrap on my snp data. I have around 5K snps and I am using R package ape: snp <- as.matrix(objt) stree = nj(dist.gene(snp)) myBoots <- boot.phylo(stree, snp, function(xx) nj(dist.gene(xx)), B = 1000, mc.cores = 6) It ha ...
R bootstrap ape written 14 months ago by User000270
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Comment: C: Variant calling for a polyploid species
... I did state the programs I am using. It is not so difficult to find the best practice etc, however I think it is not so straightforward when dealing with the polyploid species. So I wanted to know if there are some particular parameters to use or filtering etc. Thank you anyway ...
written 17 months ago by User000270
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Comment: C: Variant calling for a polyploid species
... Hi Nicolas thank you! I already did all of these steps. But I have very specific questions I stated above. ...
written 17 months ago by User000270
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Comment: C: Variant calling for a polyploid species
... Hi thanks! My chromosomes are already divided in A and B, but when I do variant calling is it nto going to result in false calls? due to the fact that it will map both on A & b? How to deal with this? ...
written 17 months ago by User000270
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Variant calling for a polyploid species
... Dear all, I am working with a tetraploid species. I have RNA-seq for varieties and a reference genome. I am going to do variant calling, possibly to study intra-varietal and inter-homoeologous SNPs. - Is it OK to do variant calling for a every variety separately is I have on average around 30K-50 ...
rna-seq snp written 17 months ago by User000270 • updated 16 months ago by archie70
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Comment: C: Tetraploid Snp Calling & Snp Filtering
... Hi, I was wondering if you found answers to the following your questions? what allele fraction should we use? Or should we call a SNP if it has at least x (high quality) reads supporting it? And what quality score (QUAL as given in the VCF output format, or any other quality measure) is suffi ...
written 17 months ago by User000270
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Comment: C: blast using python
... yes, the code above works for me, so without the error message difficult to solve ...
written 17 months ago by User000270
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Comment: C: blast using python
... on my personal experience I found it easier working with the tab delimited outputs. For a newbie in bioiformatics parsing an xml output might not be so straightforward, also if one has many sequences an xml format becomes heavier than tab. (See http://www.polarmicrobes.org/parsing-blast-xml-output/) ...
written 17 months ago by User000270
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Answer: A: blast using python
... Why complicating it so much? if you have only two sequences just use NCBI blast web site, otherwise if you will have many sequences this is not the best method, you can run either as a command line or as a bash script. #!/usr/bin/env bash BLAST="/path/to/ncbi-blast-2.2.26+/bin" REFERENC ...
written 17 months ago by User000270

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