User: shelkmike

gravatar for shelkmike
shelkmike70
Reputation:
70
Status:
Trusted
Location:
Russian Federation
Last seen:
13 hours ago
Joined:
4 years ago
Email:
s********@gmail.com

Posts by shelkmike

<prev • 10 results • page 1 of 1 • next >
1
vote
2
answers
741
views
2
answers
Comment: C: Is BUSCO really better than CEGMA for genome assembly quality evaluation?
... 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 6 months ago by shelkmike70
0
votes
2
answers
741
views
2
answers
Comment: C: Is BUSCO really better than CEGMA for genome assembly quality evaluation?
... 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 6 months ago by shelkmike70
1
vote
3
answers
1.2k
views
3
answers
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 8 months ago by shelkmike70
0
votes
1
answer
498
views
1
answers
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 8 months ago by shelkmike70
2
votes
3
answers
1.2k
views
3
answers
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 8 months ago by shelkmike70
0
votes
1
answer
498
views
1
answers
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 8 months ago by shelkmike70
6
votes
2
answers
741
views
2
answers
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 8 months ago by shelkmike70 • updated 6 months ago by h.mon20k
0
votes
1
answer
676
views
1
answers
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 23 months ago by shelkmike70
1
vote
1
answer
676
views
1
answer
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 23 months ago by shelkmike70 • updated 12 days ago by Biostar ♦♦ 20
2
votes
4
answers
2.9k
views
4
answers
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 3.7 years ago by shelkmike70

Latest awards to shelkmike

Scholar 7 months ago, created an answer that has been accepted. For A: Criteria for filtering contigs after spades assembly
Supporter 23 months ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1162 users visited in the last hour