User: rimgubaev

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rimgubaev180
Reputation:
180
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Trusted
Location:
Russia/Moscow/Skoltech
Last seen:
1 week, 2 days ago
Joined:
2 years, 6 months ago
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r********@gmail.com

Posts by rimgubaev

<prev • 98 results • page 1 of 10 • next >
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What tools to use for genetic map construction or marker ordering using large SNP datasets?
... Dear all, I have a large SNP dataset (~6K) derived from GBS sequencing of F2 intercross population and I face a problem of genetic map construction which is needed for subsequent QTl-maping. I tried famous R/qtl but first, it works quite slow, second, it does not produce a proper result in terms of ...
qtl marker ordering genetic map snp gbs written 7 weeks ago by rimgubaev180
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Which SNP callers are suitable for QTL mapping in GBS experiments with low coverage?
... Hello everyone! I am dealing with the SNP data derived from QTL-mapping (F2 progeny + parents) using GBS sequencing approach. Unfortunately, the data are of low-coverage (~5 reads per site) which is not so good considering the fact that F2 progeny is expected to have a high amount of heterozygous p ...
snp caller low-coverage qtl-mapping snp gbs written 3 months ago by rimgubaev180
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Comment: C: How to calculate number of positions covered by at least 10 times in bam file?
... Thanks, id is perfect!!! ...
written 3 months ago by rimgubaev180
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Comment: C: How to calculate number of positions covered by at least 10 times in bam file?
... Thank you, that works well! ...
written 3 months ago by rimgubaev180
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How to calculate number of positions covered by at least 10 times in bam file?
... Hello everyone! I wonder if somebody could recommend how to calculate the number of positions covered by at least 10 times in bam file? To calculate the number of positions covered by at least once in the bam file I used this oneliner: bedtools genomecov -ibam my_alignment.bam -bg | awk '{ s+=( ...
bedtools alignment coverage bam awk written 3 months ago by rimgubaev180 • updated 3 months ago by ATpoint36k
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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 6 months ago by rimgubaev180 • updated 4 months ago by Biostar ♦♦ 20
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Comment: C: intersect VCF files
... Unfortunately, I have not used GATK for this purpuses. ...
written 6 months 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 6 months 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 6 months ago by rimgubaev180 • updated 6 months ago by harold.smith.tarheel4.6k
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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 6 months ago by rimgubaev180

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Popular Question 5 weeks ago, created a question with more than 1,000 views. For Is it possible to make a PCA plot for samples using TPM exprssion values in R?
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Is it possible to make a PCA plot for samples using TPM exprssion values in R?
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Teacher 8 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 8 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 Could somebody suggest free pathway visualization tool for omics data from plants?
Popular Question 11 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 15 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 15 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 16 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 24 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 24 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 2.0 years 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 2.1 years 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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