User: rimgubaev

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rimgubaev180
Reputation:
180
Status:
Trusted
Location:
Russia/Moscow/Skoltech
Last seen:
2 days, 15 hours ago
Joined:
2 years, 2 months ago
Email:
r********@gmail.com

Posts by rimgubaev

<prev • 93 results • page 1 of 10 • next >
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How to liftover SNPs between different assemblies from different databases?
... Hello everyone! I got a quite tricky task to liftover SNPs from NCBI assembly to ENSEMBL assembly. The assemblies are different i.e. the chromosome lengths and the chromosome names. Furthermore ENSEMBL assembly is not present at NCBI and vice-versa so the using tools like NCBI Genome Remapping Serv ...
ncbi ensembl snp liftover assembly written 7 weeks ago by rimgubaev180 • updated 8 days ago by Biostar ♦♦ 20
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Comment: C: intersect VCF files
... Unfortunately, I have not used GATK for this purpuses. ...
written 9 weeks ago by rimgubaev180
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How to obtain an annotation for the list of NCBI's Gene ID?
... I wonder if someone could help to find annotation for the list of NCBI's Gene ID. I got the Gene IDs in numeric format and I want to submit the list containing IDs of interest and retrieve the annotation for this IDs from NCBI as well as references to other databases like KEGG or UniProt. ...
ncbi annotation geneid written 10 weeks ago by rimgubaev180
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Tools to filter the heterozygous SNPs with biased allele depth (AD) values in vcf file.
... Hello everyone! There is the following problem in my vcf file produced by GATK: a large proportion of heterozygous sites has a bias in allele depth values (AD). For example, AD is 43,7 which means that the 43 reads support one allele while 7 support another. In order to avoid possible false calls in ...
vcf gatk allele depth ad heterozygous snps written 10 weeks ago by rimgubaev180 • updated 10 weeks ago by harold.smith.tarheel4.5k
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Heterozygous calls (SNPs) problem while working with inbred lines.
... Hello everyone! I faced the problem similar to one [previously discussed][1]. However, I still did not get what is the common or generally accepted practice to deal with suspiciously frequent occurrence of heterozygous SNPs in multisample vcf file for inbred lines. For me, there is at least one obv ...
vcf snps gatk heterozygous sequencing errors written 10 weeks ago by rimgubaev180
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Comment: C: Using Gatk On Inbred Species - What To Do With The Heterozygous Calls?
... Do you simply remove them? And if so if there are some publications where the similar filter is applied? ...
written 10 weeks ago by rimgubaev180
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Which option is better for variance component estimation in TASSEL?
... Hello everyone! There are two options in TASSEL for variance component estimation while running a mixed linear model (MLM) for association mapping. First one is to use P3D compression, second is to re-estimate variance after each marker. TASSEL help window claims that the compression saves time a ...
variance gwas p3d tassel mlm written 11 weeks ago by rimgubaev180 • updated 10 weeks ago by Biostar ♦♦ 20
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Comment: C: Is it ok to use median instead of mean for phenotype data in GWAS studies?
... It's not so many actually, it is 7%. ...
written 11 weeks ago by rimgubaev180
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Is it ok to use median instead of mean for phenotype data in GWAS studies?
... Hello everyone! I wonder if somebody could suggest me an article related or the solution to the following problem. I got phenotype data collected for the plant of interest for three years to run GWAS. For some samples phenotype data failed to pass Shapiro-Wilk test for normality so I want to use the ...
gwas phenotype data association written 11 weeks ago by rimgubaev180
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What is optimal distance to scan for genes near SNPs for pathway overrepresentation analysis?
... Hello everyone! I want to perform the pathway overrepresentation analysis using the SNP dataset. I got over 100 SNPs significantly associated with the trait of interest and I want to find the genes that are potentially related to these SNPs and include them into pathway overrepresentation analysis. ...
pathways snpeff pathway analysis snp gwas written 3 months ago by rimgubaev180

Latest awards to rimgubaev

Voter 10 weeks ago, voted more than 100 times.
Teacher 4 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 4 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?
Popular Question 11 months 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 11 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?
Scholar 12 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?
Supporter 12 months ago, voted at least 25 times.
Scholar 20 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 20 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 20 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 21 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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