User: rimgubaev
rimgubaev • 180
- Reputation:
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- Russia/Moscow/Skoltech
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- 1 week, 2 days ago
- Joined:
- 2 years, 6 months ago
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Posts by rimgubaev
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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 7 weeks ago by
rimgubaev • 180
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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 3 months ago by
rimgubaev • 180
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... Thanks, id is perfect!!! ...
written 3 months ago by
rimgubaev • 180
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... Thank you, that works well!
...
written 3 months ago by
rimgubaev • 180
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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 6 months ago by
rimgubaev • 180
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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 6 months ago by
rimgubaev • 180
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... 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 ...
written 6 months ago by
rimgubaev • 180
• updated
6 months ago by
harold.smith.tarheel • 4.6k
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... 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 ...
written 6 months ago by
rimgubaev • 180
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