User: rimgubaev
rimgubaev • 200
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Posts by rimgubaev
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... 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 ...
written 8 days ago by
rimgubaev • 200
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... 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 ...
written 4 months ago by
rimgubaev • 200
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... 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 ...
written 8 months ago by
rimgubaev • 200
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... 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 ...
written 10 months ago by
rimgubaev • 200
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... Thanks, id is perfect!!! ...
written 10 months ago by
rimgubaev • 200
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... Thank you, that works well!
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written 10 months ago by
rimgubaev • 200
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... 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+=( ...
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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 13 months ago by
rimgubaev • 200
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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 13 months ago by
rimgubaev • 200
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