User: rimgubaev

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rimgubaev200
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200
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Russia/Moscow/Skoltech
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3 years, 1 month ago
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Posts by rimgubaev

<prev • 100 results • page 1 of 10 • next >
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How to formally test the replicate consistency having genotype data?
... I have vcf file where each plant line is represented by 3 technical replicates. To show that my replicates are consistent I did PC analysis and visualized the results by plotting PC1 vs PC2 and coloring the replicates of the lines. On a plot the replicates of the same line cluster closer than the re ...
replicates vcf consistency snp genetic variance written 8 days ago by rimgubaev200
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Are there tools for SNP remapping (liftover) for non-model organism or ones that do not require chain file?
... Dear all I wonder if there is a tool that allows remapping SNPs from one assembly to another in one step? The solutions that I identified to solve this problem are either work with model organisms like [NCBI Genome Remapping Service][1] or require a chain file like [LiftOver][2] that are available ...
vcf assembly snp liftover chain file written 4 months ago by rimgubaev200
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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 8 months ago by rimgubaev200
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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 10 months ago by rimgubaev200
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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 10 months ago by rimgubaev200
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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 10 months ago by rimgubaev200
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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 10 months ago by rimgubaev200 • updated 10 months ago by ATpoint46k
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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 13 months ago by rimgubaev200 • updated 11 months ago by Biostar ♦♦ 20
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Comment: C: intersect VCF files
... Unfortunately, I have not used GATK for this purpuses. ...
written 13 months ago by rimgubaev200
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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 13 months ago by rimgubaev200

Latest awards to rimgubaev

Teacher 4 days ago, created an answer with at least 3 up-votes. For A: Are there some ways to extract information in tabular format from text with regu
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Popular Question 6 weeks ago, created a question with more than 1,000 views. For Are there any journals that accept short transcriptome announcements?
Popular Question 3 months 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 3 months 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 3 months ago, created a question with more than 1,000 views. For Are there any journals that accept short transcriptome announcements?
Popular Question 3 months ago, created a question with more than 1,000 views. For Why volcano plot has no points in the middle of plot?
Popular Question 6 months 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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Popular Question 18 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 18 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 22 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?
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