User: Mensur Dlakic

gravatar for Mensur Dlakic
Mensur Dlakic600
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600
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Location:
USA
Website:
http://www.montana.edu...
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Google Scholar Page
Last seen:
11 minutes ago
Joined:
1 month, 4 weeks ago
Email:
m************@gmail.com

Posts by Mensur Dlakic

<prev • 75 results • page 2 of 8 • next >
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Answer: A: What methods can be used to identify chemolithotrophs in 16S data?
... One way to do it is to add 16S rRNA sequences of know chemolithotrophs and non-chemolithotrophs to your data, and build a phylogenetic tree. The sequences from your data that group together with know chemolithotrophs are more likely to be in the same category. ...
written 8 days ago by Mensur Dlakic600
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Comment: C: standalone CDsearch version?
... Links to pre-formatted databases for RPS-BLAST are shown in [**this section**][1]. [1]: https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml#RPSBFtp ...
written 8 days ago by Mensur Dlakic600
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Answer: A: How to prepare high-resolution protein secondary structures diagrams?
... I think [**Procheck**][1] or its online [**server**][2] have some of the properties you need, but the plot is spread out over several pages. You may want to check out the residue property plot in online version, and scroll down until you find the cartoon. It shows residue solvent accessibility as we ...
written 9 days ago by Mensur Dlakic600
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Comment: C: How I update makeblastdb
... Setting/exporting `PATH` variable does not work instantly in the same session. You need to log out and back in, or open a new session. To find out which binary is executed by system, type `which makeblastdb`. After logging back in, that should change to the new binary if you have set the `PATH` corr ...
written 9 days ago by Mensur Dlakic600
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Comment: C: CheckM and strain heterogeneity
... The only thing I can conclude from this graph is that you have 7 pure bins that are very incomplete. Why are they incomplete? Because they have at most 30% of marker genes present in single copy, and other marker genes are missing. That's what the gray-bar legend is telling you, and it seems pretty ...
written 11 days ago by Mensur Dlakic600
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Comment: C: CheckM and strain heterogeneity
... I think at some point you need to learn how to interpret these graphs rather than expecting me to explain you everything, and especially so because my explanations seem not to be working. The meaning of bars and colors underneath is linked to the number of marker genes that are found in a bin. Let' ...
written 11 days ago by Mensur Dlakic600
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Comment: C: CheckM and strain heterogeneity
... [**This paper**][1] deals with completeness criteria for MAGs. [1]: https://www.ncbi.nlm.nih.gov/pubmed/28787424 ...
written 12 days ago by Mensur Dlakic600
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Comment: C: CheckM and strain heterogeneity
... All of your double-digit bins and `bin_6` have low completeness. However starting with `bin_8` and everything below it, you have at least 70% complete (meta)genomes. The question is whether you can separate those bins better to get a cleaner picture. Don't know how you did binning, but try a more st ...
written 12 days ago by Mensur Dlakic600
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Comment: C: Improving assembly via normalizing reads
... I was primarily referring to binning **AFTER** the assembly. In addition to aforementioned BlobTools, there is nice implementation using self-organizing maps in [**Binning**][1]. I typically use a custom [**t-SNE**][2] pipeline. See the supplementary material of [**this paper**][3] to get an idea wh ...
written 13 days ago by Mensur Dlakic600
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Comment: C: Improving assembly via normalizing reads
... Have you done binning on your original assembly? That would remove bacterial contigs after the assembly, which is still fine. Also, taxonomic partitioning can be done using [**BlobTools**][1]. Though your coverage is impressive, I'd be hesitant to throw away any data before the assembly as any inc ...
written 13 days ago by Mensur Dlakic600

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