User: vijinim

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vijinim90
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Posts by vijinim

<prev • 17 results • page 1 of 2 • next >
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Answer: A: Binning Tools for Long Reads/Contigs
... I found a tool named [MEGAN-LR][1] which can bin metagenomic long reads and contigs. Although it is based on taxonomical binning, I'm going to try it and see. Thank you all for your insights and ideas. :) [1]: https://biologydirect.biomedcentral.com/articles/10.1186/s13062-018-0208-7 ...
written 3 days ago by vijinim90
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Comment: C: Binning Tools for Long Reads/Contigs
... Thank you very much. I will try it and see. :) ...
written 3 days ago by vijinim90
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Comment: C: Binning Tools for Long Reads/Contigs
... Yes. I think this is the issue. I will find another software to do binning. Thank you very much for your insights and explanations. :) ...
written 3 days ago by vijinim90
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Comment: C: Binning Tools for Long Reads/Contigs
... I used Escherichia coli CFT073 and Staphylococcus aureus JP080. When we get short reads and bin the contigs, MaxBin produces 2 bins with good results. Similarly, I tried MaxBin with long reads from the same 2 genomes but it gave only 1 bin. ...
written 9 days ago by vijinim90
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Comment: C: Binning Tools for Long Reads/Contigs
... I believe there is no difference apart from the effects of the error rates of short reads and long reads. However, I tried to bin a simulated dataset of reads from 2 bacterial genomes (with 20kb - 21kb read lengths and 10% error rate) and the tool failed to identify two bins. It produced only one ...
written 11 days ago by vijinim90
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Binning Tools for Long Reads/Contigs
... Majority of the currently available metagenomics binning tools are designed to work with short reads and contigs obtained from short reads. Does someone know if there are any tools available to bin long reads or contigs obtained from long reads? Thank you very much! :) ...
long reads metagenomics contigs binning written 12 days ago by vijinim90
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Comment: C: Where can I find publicly available metagenomics contig datsets?
... Thank you very much. This is very helpful. :) ...
written 18 days ago by vijinim90
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Comment: A: Where can I find publicly available metagenomics contig datsets?
... I did not find any annotated datasets up to now. What researchers have done is obtain a publicly available set of reads, assemble it using an assembly software, obtain the contigs and use the tool [TAXAassign v0.4][1] to determine the origin species of these contigs. [1]: https://github.com/umer ...
written 4 weeks ago by vijinim90
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Comment: C: Getting an error whilst trying to import Biopython SeqIO
... Is this [post][1] related to your problem? You can have a look. [1]: https://stackoverflow.com/questions/51296034/importerror-cannot-import-name-aligners-biopython ...
written 8 weeks ago by vijinim90
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Where can I find publicly available metagenomics contig datsets?
... I'm searching for a publicly available **metagenomics *contig* dataset** which has information regarding which contig came from which species and the assembler used. If anyone knows, can you kindly point me to the reasources? Thank you very much! :) ...
metagenomics contigs datasets written 9 weeks ago by vijinim90 • updated 27 days ago by Jonathanjacobs210

Latest awards to vijinim

Student 4 weeks ago, asked a question with at least 3 up-votes. For What is differential abundance analysis?
Student 4 weeks ago, asked a question with at least 3 up-votes. For Binning of reads vs. binning of contigs in metagenomics
Supporter 3 months ago, voted at least 25 times.

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