User: rimgubaev

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rimgubaev120
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120
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Russia/Moscow/Skoltech
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6 days, 18 hours ago
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1 year, 4 months ago
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Posts by rimgubaev

<prev • 56 results • page 1 of 6 • next >
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How to interpret slash (/) and vertical pipe (|) in GATK's vcf output?
... 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 & ...
vcf gatk formatting written 23 days ago by rimgubaev120 • updated 23 days ago by h.mon26k
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Has anyone dealt with "Specified element is out of bounds" error produced by TASSEL?
... 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) ...
mixed linear model gwas tassel mlm written 23 days ago by rimgubaev120
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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 rimgubaev120
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Which R packages are fit for calculating distances and make phylogenetic trees from VCF files?
... 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. ...
vcf phylogeny rna-seq populational genetics trees written 4 weeks ago by rimgubaev120
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Which test is applied in order to generate p-values in TASSEL when using Mixed Linear Model?
... 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 ...
gwas tassel statistical test written 5 weeks ago by rimgubaev120 • updated 16 days ago by Biostar ♦♦ 20
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Can I build a phylgenetic tree using SNPs obtained by differen techniques?
... 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 ...
array gbs snp population genetics written 7 weeks ago by rimgubaev120
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Comment: C: Why switch negative values in kinship matrix to zeros?
... 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 rimgubaev120
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Why switch negative values in kinship matrix to zeros?
... 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 ...
spagedi kinship tassel population genetics written 8 weeks ago by rimgubaev120 • updated 8 weeks ago by Asaf5.7k
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Comment: C: How to merge multiple fastq file using table?
... 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 rimgubaev120
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How to merge multiple fastq file using table?
... 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 ...
fastq cat bash written 8 weeks ago by rimgubaev120

Latest awards to rimgubaev

Popular Question 7 weeks ago, created a question with more than 1,000 views. For How to extract all promoter regions in multi-fasta format from genome using GFF?
Scholar 8 weeks ago, created an answer that has been accepted. For A: How to extract all promoter regions in multi-fasta format from genome using GFF?
Scholar 3 months ago, created an answer that has been accepted. For A: How to extract all promoter regions in multi-fasta format from genome using GFF?
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Scholar 10 months ago, created an answer that has been accepted. For A: How to extract all promoter regions in multi-fasta format from genome using GFF?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How to extract all promoter regions in multi-fasta format from genome using GFF?
Scholar 10 months ago, created an answer that has been accepted. For A: How to extract all promoter regions in multi-fasta format from genome using GFF?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: How to extract all promoter regions in multi-fasta format from genome using GFF?

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