User: shelkmike
shelkmike • 70
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Posts by shelkmike
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... Thank you, I have already read the article, but haven't found a clear answer there. I supposed, maybe some of BioStars' members have a more unambiguous answer. ...
written 5 months ago by
shelkmike • 70
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... Thank you for your response. I'll try to reformulate in simpler words:
1) The CEGMA's protein set has a shortcoming of having too few proteins (248, to be precise)
2) The BUSCO's sets shortcoming is that they contain proteins that are single-copy in 90% of species, not 100%.
Why is it a commonpla ...
written 5 months ago by
shelkmike • 70
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... 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 6 months ago by
shelkmike • 70
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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 7 months ago by
shelkmike • 70
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... 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 7 months ago by
shelkmike • 70
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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 7 months ago by
shelkmike • 70
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... 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 ...
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... 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 21 months ago by
shelkmike • 70
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... 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 ...
written 21 months ago by
shelkmike • 70
• updated
21 months ago by
Brice Sarver • 2.4k
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... 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 3.6 years ago by
shelkmike • 70
Latest awards to shelkmike
Scholar
5 months ago,
created an answer that has been accepted.
For A: Criteria for filtering contigs after spades assembly
Supporter
21 months ago,
voted at least 25 times.
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