User: rimgubaev

gravatar for rimgubaev
rimgubaev140
Reputation:
140
Status:
Trusted
Location:
Russia/Moscow/Skoltech
Last seen:
14 hours ago
Joined:
1 year, 8 months ago
Email:
r********@gmail.com

Posts by rimgubaev

<prev • 71 results • page 1 of 8 • next >
1
vote
0
answers
70
views
0
answers
Could someone recommend courses/workshops on plant quantitative genetics?
... Hello everyone! I am trying to find courses/workshops devoted to GWAS and QTL mapping of quantitative traits in plants, yet with no success. I am interested mostly in data analysis and theory, not experimental design. I would be very grateful if someone suggests some courses planned for 2020 or bett ...
workshops gwas qtl mapping courses plant genomics written 1 day ago by rimgubaev140
0
votes
1
answer
61
views
1
answer
Is there any command line or GUI software to find SSR microsatellites using pattern?
... Hello everyone! The problem is the following: I got a pattern of microsatellite, for example (GA)8nGTGT(G)11, and I want to search for all possible targets across the specified locus (2nd chromosome) across all genome assemblies. I tried non-specific software namely BLASTn, however there is no optio ...
ssr microsatellites hordeum vulgare written 13 days ago by rimgubaev140 • updated 13 days ago by Pierre Lindenbaum123k
0
votes
0
answers
122
views
0
answers
Comment: C: How to extract promoter sequences from a plant draft genome?
... Yeah, that's correct, thanks! ...
written 4 weeks ago by rimgubaev140
2
votes
0
answers
122
views
0
answers
Comment: C: How to extract promoter sequences from a plant draft genome?
... I faced the same problem around year ago working with Nicotiana tabacum genome (annotated scaffolds). At that time I did not find the solution so just tried to write my own bash script that utilizes the common software like samtools and bed tools and outputs multi fasta with promoter sequences. Here ...
written 4 weeks ago by rimgubaev140
0
votes
0
answers
67
views
0
answers
Why kinship is a random effect while population structure is a fixed effect in GWAS studies?
... Hello everyone! The mixed linear models frequently applied for GWAS account for confounding factors like fixed (population structure) and random effects (kinship). I am confused with the following thing: The population structure information for example PCs are calculated based on genotype data and k ...
principle components gwas kinship matrix mlm written 4 weeks ago by rimgubaev140
0
votes
0
answers
97
views
0
answers
What kind of approaches are used in order to estimate average size of LD block using LD-decay plot?
... I wonder if someone could give examples of how one could estimate the average size of LD block by looking at LD decay plot like one attached. I know that it is possible to set a certain threshold for *r2*, but it is not clear which value should be used then. For example, I just pick *r2* equal to ...
linkage disequilibrium snp r2 ld block written 4 weeks ago by rimgubaev140
0
votes
4
answers
6.4k
views
4
answers
Comment: C: intersect VCF files
... I also would like to add that in order to obtain a vcf file containing information for common SNPs for samples from file 1.vcf.gz and 2.vcf.gz the following command should be used: bcftools merge --merge all 0002.vcf.gz 0003.vcf.gz > merged.vcf ...
written 5 weeks ago by rimgubaev140
0
votes
0
answers
85
views
0
answers
What does the exclamation mark (!) means in Haploview output?
... Hello everyone! I wonder if someone could explain what does the exclamation mark (!) means in the Haploview output in example below (see marker #31): BLOCK 3. MARKERS: 31! 32 33 34 3111 (0.655) |0.646 0.000 0.003| 4433 (0.344) |0.298 0.033 0.003| It is also marked with triangle (see m ...
haploview ld haploblocks written 12 weeks ago by rimgubaev140
0
votes
0
answers
85
views
0
answers
Is it possible to assign haplotypes to individuals using haploview?
... Hello everyone! I wonder if there is a way to extract a haplotypes calculated by Haploview software into the following table: Sample | Block1 | Block2 | etc. | --------- | ---------- | ---------- | ---------- | ind1 | 42312132 | 11214 | ..... | ind ...
vcf haplotype blocks haploview ld plink written 12 weeks ago by rimgubaev140
0
votes
0
answers
131
views
0
answers
How to convert vcf to SPAGeDi input format?
... Hello everyone! I got filtered VCF file with SNPs produced by GATK and I want to make kinship matrix in SPAGeDi. I tried to format my VCF using NGSToolsApp but it produces file which seem to be truncated since I can't open it in gedit and SPAGeDi (I use version 1.3a available for linux) also produce ...
vcf spagedi kinship written 3 months ago by rimgubaev140 • updated 6 weeks ago by Biostar ♦♦ 20

Latest awards to rimgubaev

Popular Question 5 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 6 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 7 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 7 months ago, voted at least 25 times.
Scholar 14 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 14 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 14 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 15 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?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1125 users visited in the last hour