User: shelkmike

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shelkmike40
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Posts by shelkmike

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Comment: C: Criteria for filtering contigs after spades assembly
... Also, I must note that your coverage is low. For bacterial genome assembly, average genome coverage of at least 50x is preferred. By the way, I assembled many bacterial genomes and have never seen such a heterogeneous coverage as in your diagram. Really looks like a mixture of genomes of several spe ...
written 28 days ago by shelkmike40
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Answer: A: Fastq files quality
... First of all, if it drops to 34 or so, this is not a problem - 34 is pretty good quality (it implies that the probability of error is about 0.0004) . I always see this drop in reads from HiSeq 2000. My colleagues explained it to me long ago - as far as I remember, this is because the sequencing mach ...
written 4 weeks ago by shelkmike40
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Answer: A: Criteria for filtering contigs after spades assembly
... If you're afraid of contamination or spurious sequencing products, I suggest to align by BLAST all of the contigs to some reference (or even to the NCBI NT or NCBI NR databases entirely), to decide which of the contigs are "Ok" (i.e. have matches to the species you are interested in). Then you can p ...
written 4 weeks ago by shelkmike40
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Comment: C: Fastq files quality
... Please specify: 1) How deep is this drop (to what Q-score does the quality fall)? 2) Does the quality recover after this drop? I mean, does it remain low till the end of reads or it rises to normal values after the drop? 3) At what base from the beginning of reads does this drop occur? I mean, numbe ...
written 4 weeks ago by shelkmike40
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Is BUSCO really better than CEGMA for genome assembly quality evaluation?
... BUSCO is a successor to CEGMA and is often spoken about as being superior. However, I doubt that this is so. The thing is that CEGMA uses a set of ultra-conservative genes - the ones that are present in human, mouse, fruit fly, nematode, arabidopsis and yeasts. On the contrary, BUSCO uses genes that ...
cegma busco genome assembly written 4 weeks ago by shelkmike40
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Comment: C: Phylogeny from incomplete orthogroups
... Thank you for your response. The aim of the work is simply to build a correct tree of species. Information from only 'complete' orthogroups is insufficient for this, due to a low number of such orthogroups. > If you use your approach and replace missing sequences with all gaps (or Ns), there wi ...
written 15 months ago by shelkmike40
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Phylogeny from incomplete orthogroups
... Hello, everyone. I'm building a phylogenetic tree from sequenced transcriptomes of 100 species. I've calculated orthogroups by OrthoMCL and will build a tree by RAxML. In the most articles I've seen that authors take for tree building only those orthogroups, which have exactly one gene from each s ...
phylogenetics orthogroups orthomcl rna-seq written 15 months ago by shelkmike40 • updated 15 months ago by Brice Sarver2.4k
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Answer: A: Mapsembler2 targeted micro assembly and visualization of the local assembly grap
... Hi Pierre! Mapsembler is a useful program, I use it since it's first version (my paper citing it will be published soon). However, I think, mapsembler needs a more detailed manual, describing more thoroughly its parameters and algorithm. Especially, I would like to ask (about Mapsembler2  ver 2.2. ...
written 3.1 years ago by shelkmike40

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