User: Sergey Naumenko

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Posts by Sergey Naumenko

<prev • 15 results • page 1 of 2 • next >
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Comment: C: 1000genomes: choosing the best annotation from multiple transcripts
... Of course, you can just use information about substitutions (variants) from the annotation. The annotation program should know about coding and non-coding regions. If you want just to calculate pn/ps ratio as exercise and forget about it, it is ok to parse annotation. But I would not recommend th ...
written 11 days ago by Sergey Naumenko170
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Comment: C: 1000genomes: choosing the best annotation from multiple transcripts
... Yes, those are different transcripts (isoforms). See [DMD][1] gene, for example. You can limit your output to only canonical ones (should be 1 canonical isoform for a gene) with -canon option in [SNPeff][2]. In that case you can just trust SNPeff, what it will put there. The other option is to us ...
written 13 days ago by Sergey Naumenko170
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Answer: A: 1000genomes: choosing the best annotation from multiple transcripts
... Hi spiral01! What a brave scientist you are! (I mean, so many people were working to find selection in humans before). As to the point, you'd better start from the other end: to identify regions of the genome you are interested to study. It looks like you are interested in the protein coding gen ...
written 13 days ago by Sergey Naumenko170
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Answer: A: Is there any way to install RStudio (or any other powerful IDE for R) without ro
... Hi dark_rider_2010! Have you tried, instead of trying to hack the system, to understand your sysadmin? Even if you install R-studio, which is possible, your sysadmin will figure it out very soon, and ... will get angry. When I was an angry sysadmin, I was definitely against the installation of R-s ...
written 14 days ago by Sergey Naumenko170
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Answer: A: VCFTools vcf-merge not merging all files
... Hi Zihan! * Switch to bcltools - it is faster, and (hopefully) has less bugs. [bcftools][1] * Check sample names in your vcf files: for f in *.gz;do echo $f; bcftools query -l $f;done; If you are trying to create a multisample vcf file (to merge vcf files), and you have the same sample names ...
written 15 days ago by Sergey Naumenko170
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Comment: C: VCFTools vcf-merge not merging all files
... Hi Zihan! How about - checking sample names - are they all different? - using bcftools merge - to remove all annotations, merge, and annotate then Good luck! Sergey ...
written 15 days ago by Sergey Naumenko170
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Answer: A: Zero length branches on a phylogram
... Hi Nancy! 1. Try to exclude mouse branch from the analysis - maybe your method is sensitive to the case with 2 almost identical sequences? 2. Are you aligning amino acids sequences or DNA? With DNA you will have larger divergence, because synonymous substitutions will be counted (however, dependin ...
written 18 days ago by Sergey Naumenko170
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Comment: C: STAR Alignment Trouble
... It looks like it can't find your input files. Check the path - it is case sensitive. ...
written 3 months ago by Sergey Naumenko170
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Answer: A: STAR Alignment Trouble
... Hi! It is hard to guess. Maybe you are mapping to the wrong reference, or you sample is contaminated? Do you see any error messages from STAR? What is your mapping statistics? Maybe try to add --outReadsUnmapped Fastx to see how big are unmapped files? Other parameters you might find useful: [rna ...
written 3 months ago by Sergey Naumenko170
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Answer: A: How identify zero fold degradation sites
... "Zero fold degenerate site" looks like an incorrect term. The correct ones are 'fourfold degenerate' and 'twofold degenerate': [Genetic code][1]. The corresponding question has been already answered [for example, here][2] [1]: https://en.wikibooks.org/wiki/An_Introduction_to_Molecular_Biology/Ge ...
written 3 months ago by Sergey Naumenko170

Latest awards to Sergey Naumenko

Scholar 11 days ago, created an answer that has been accepted. For A: multisample SNP calling in plants
Scholar 14 days ago, created an answer that has been accepted. For A: multisample SNP calling in plants
Scholar 16 days ago, created an answer that has been accepted. For A: multisample SNP calling in plants
Scholar 3 months ago, created an answer that has been accepted. For A: multisample SNP calling in plants

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