User: rimgubaev
rimgubaev • 120
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Posts by rimgubaev
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... The GATK output vcf file contains genotypes in which alleles could be separated both by vertical bar ("|") and slash symbols ("/"). For example: 0/1, 0|1, 0/0, 1|1. I found the explanation at [EBI][1] portal. It is said that
> The vertical pipe | indicates that the genotype is phased, and is
& ...
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... I try to run Mixed linear model (MLM) in TASSEL on my 87 individual dataset (in 3 replicates each, 261 accessions in total). When I add a factor variable (with 87 levels, respectively) that indicate number of replicate for each accessions I got an error "Specified element is out of bounds: (0 , 189) ...
written 23 days ago by
rimgubaev • 120
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Comment:
A: Convert RefseqID to EntrezID
... Maybe UniProt Retrive/ID mapping is user-friendly and could help: https://www.uniprot.org/uploadlists/
You can submit list of RefSeq ID and then add a Entrez column to output table and then download it.
...
written 4 weeks ago by
rimgubaev • 120
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... Hello everyone!
Please suggest some R packages for calculating distances and make phylogenetic trees from VCF files. I am searching for package with clear manual/tutorial and broad number of methods to calculate genetic distances and tree building, bootstrapping.
Thank you. ...
written 4 weeks ago by
rimgubaev • 120
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... Hello everyone!
I could not find the statistical test which is utilized by TASSEL when running mixed liner model to find SNP-phenotype association.
Googling on this topic had no success:
The article on TASSEL (https://tassel.bitbucket.io/docs/bradbury2007bioinformatics.pdf) say that F-test is utili ...
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... I had GBS libraries for several plant lines then I performed SNP calling using GATK pipeline. So my question is the following: is it appropriate to compare obtained SNPs with SNPs obtained in other studies by arrays or RAD-seq for example? Namely I want to build a phylogenetic tree and see how my p ...
written 7 weeks ago by
rimgubaev • 120
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... Thanks! But still it is not clear why kinship matrix produced by Tassel contains negative values as well as why this values not in range from 0 to 1 i.e. there are numbers that are actually larger than 1. If someone could explain It would be great. Unfortunately I didn't find the relevant explanatio ...
written 8 weeks ago by
rimgubaev • 120
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... I'm quite new to population genetics and recently looked at these papers and found that the negative values in kinship matrix are switched to zeros.
https://www.nature.com/articles/srep41561
> The relative kinship matrix comparing all pairs of accessions was
> calculated using the software p ...
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... This is a nice one! I did exactly the same script containing many cat command rows in R since I'm not a good bash user. ...
written 8 weeks ago by
rimgubaev • 120
14
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245
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... I got the following table containing sample names and corresponding replicates like this:
Sample Replicate
S1 r12
S1 r25
S1 r68
S2 r58
S2 r34
S4 r13
etc.
In the folder I got the corresponding fastq files (for example: r12.fastq). The total am ...
written 8 weeks ago by
rimgubaev • 120
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