User: Sergey Naumenko

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Posts by Sergey Naumenko

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Answer: A: What tools are proper for plant genome pre- and post-assembly and annotation of
... Hi bioinformatics_bel! What a brave researchers you are to work with those huge genomes! I'm afraid there is no pine- or birch- specific tools, or any universal software for that genome size. I hope you are aware of the Norway spruce genome project (https://www.nature.com/articles/nature12211) and ...
written 6 hours ago by Sergey Naumenko210
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Answer: A: excel and most up/down regulated
... Dear candidasusae, Differential expression analysis is one of the most elaborated analyses in bioinformatics, with excellent guidelines and packages available. I'd suggest reading one of those to improve your analysis, because if you are going to publish the results, you'd like to use reproducible ...
written 1 day ago by Sergey Naumenko210
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Answer: A: Longer scaffolds from multiple eukaryote genome assemblies
... Hi Eric! Maybe you have already done this, I'd align the two genomes first to see a synteny map. And depending on what you see, I'd plan the assembly. For the alignment Mummer (http://mummer.sourceforge.net/) may help, or another tool. Sergey ...
written 2 days ago by Sergey Naumenko210
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Answer: A: Phylogenetic tree from denovo assemblies
... Hello Samuel! Not sure about neat and quickly. It depends on the biology of your species. With very small genomes (viruses, 10k) you may try to 1. make a multiple alignment of whole genomes with muscle (https://www.drive5.com/muscle/) or another aligner, and then 2. build a phylogenetic tree ...
written 5 days ago by Sergey Naumenko210
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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 4 months ago by Sergey Naumenko210
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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 4 months ago by Sergey Naumenko210
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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 4 months ago by Sergey Naumenko210
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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 4 months ago by Sergey Naumenko210
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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 4 months ago by Sergey Naumenko210
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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 4 months ago by Sergey Naumenko210

Latest awards to Sergey Naumenko

Scholar 4 months ago, created an answer that has been accepted. For A: multisample SNP calling in plants
Scholar 4 months ago, created an answer that has been accepted. For A: multisample SNP calling in plants
Scholar 4 months ago, created an answer that has been accepted. For A: multisample SNP calling in plants
Scholar 7 months ago, created an answer that has been accepted. For A: multisample SNP calling in plants

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