User: rimgubaev
rimgubaev • 180
- Reputation:
- 180
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- Location:
- Russia/Moscow/Skoltech
- Last seen:
- 2 days, 15 hours ago
- Joined:
- 2 years, 2 months ago
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Posts by rimgubaev
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... 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 ...
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Comment:
C: intersect VCF files
... Unfortunately, I have not used GATK for this purpuses. ...
written 9 weeks ago by
rimgubaev • 180
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... 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. ...
written 10 weeks ago by
rimgubaev • 180
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... 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 ...
written 10 weeks ago by
rimgubaev • 180
• updated
10 weeks ago by
harold.smith.tarheel • 4.5k
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... 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 ...
written 10 weeks ago by
rimgubaev • 180
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... Do you simply remove them? And if so if there are some publications where the similar filter is applied? ...
written 10 weeks ago by
rimgubaev • 180
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... 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 ...
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... It's not so many actually, it is 7%. ...
written 11 weeks ago by
rimgubaev • 180
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... 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 ...
written 11 weeks ago by
rimgubaev • 180
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... 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. ...
written 3 months ago by
rimgubaev • 180
Latest awards to rimgubaev
Popular Question
4 weeks ago,
created a question with more than 1,000 views.
For Could somebody suggest free pathway visualization tool for omics data from plants?
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10 weeks ago,
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For A: How to extract all promoter regions in multi-fasta format from genome using GFF?
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For A: How to extract all promoter regions in multi-fasta format from genome using GFF?
Popular Question
7 months ago,
created a question with more than 1,000 views.
For Could somebody suggest free pathway visualization tool for omics data from plants?
Popular Question
7 months ago,
created a question with more than 1,000 views.
For Could somebody suggest free pathway visualization tool for omics data from plants?
Popular Question
11 months ago,
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For How to extract all promoter regions in multi-fasta format from genome using GFF?
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11 months ago,
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For A: How to extract all promoter regions in multi-fasta format from genome using GFF?
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For A: How to extract all promoter regions in multi-fasta format from genome using GFF?
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20 months ago,
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For A: How to extract all promoter regions in multi-fasta format from genome using GFF?
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20 months ago,
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For A: How to extract all promoter regions in multi-fasta format from genome using GFF?
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20 months ago,
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For A: How to extract all promoter regions in multi-fasta format from genome using GFF?
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21 months ago,
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For A: How to extract all promoter regions in multi-fasta format from genome using GFF?
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