User: rimgubaev
rimgubaev • 140
- Reputation:
- 140
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- Russia/Moscow/Skoltech
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- 14 hours ago
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- 1 year, 8 months ago
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Posts by rimgubaev
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... 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 ...
written 1 day ago by
rimgubaev • 140
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... 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 ...
written 13 days ago by
rimgubaev • 140
• updated
13 days ago by
Pierre Lindenbaum ♦ 123k
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... Yeah, that's correct, thanks! ...
written 4 weeks ago by
rimgubaev • 140
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... 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
rimgubaev • 140
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... 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 ...
written 4 weeks ago by
rimgubaev • 140
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... 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 ...
written 4 weeks ago by
rimgubaev • 140
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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
rimgubaev • 140
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85
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... 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 ...
written 12 weeks ago by
rimgubaev • 140
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85
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... 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 ...
written 12 weeks ago by
rimgubaev • 140
0
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131
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... 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 ...
Latest awards to rimgubaev
Popular Question
7 weeks 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 weeks 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
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,
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For A: How to extract all promoter regions in multi-fasta format from genome using GFF?
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7 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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14 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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14 months ago,
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For A: How to extract all promoter regions in multi-fasta format from genome using GFF?
Scholar
14 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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15 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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