User: jesselee516

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jesselee516100
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Posts by jesselee516

<prev • 28 results • page 1 of 3 • next >
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Comment: C: How similar could be between Bacteria haplotype in term of SNPs?
... Thanks, your answer really make sense. ...
written 11 months ago by jesselee516100
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Comment: C: How similar could be between Bacteria haplotype in term of SNPs?
... Yes, '*are you asking how many SNPs one strain can have versus another to still be classified as the same strain/species?*'. That is basically my question. Or I can ask: 'normally, what percentages of SNPs are shared between strains under the same species' ...
written 12 months ago by jesselee516100
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How similar could be between Bacteria haplotype in term of SNPs?
... Hi all, I had a question about the bacteria haplotypes(may be called strain? not sure here). We usually measure the SNPs for that haplotypes. For example, we have two haplotypes for one bacteria species, haplotype1 and haplotype2. How similarity could be these two haplotypes in term of shared SNPs ...
genome metagenomics bacteria snp written 14 months ago by jesselee516100
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Comment: C: bowtie2 paired end insertion length
... Thank you so much. The result now is reasonable. I changed the parameters to -I 200 and -X 1000, then the result is 100% concordantly(98.61% exactly 1 time, and 1.39% greater than 1 times.). I will accept your solution for this post. Thanks again!!! ...
written 2.1 years ago by jesselee516100
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Comment: C: bowtie2 paired end insertion length
... Thanks a lot. I add two parameters(-I 500 -X 700). Because I simulated 100bp paired end reads with 400bp insertion length. My fragments should be 600bp(400bp+100bp*2), is that correct? And the std is 50bp. So 500bp to 700bp is already mean with 2*std. Now I get '***1618473 (94.45%) aligned concordan ...
written 2.1 years ago by jesselee516100
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Comment: C: bowtie2 paired end insertion length
... Thanks for reply. Do you any suggestion for me in this case? Does that will cause problem? I use DWGSIM to simulate reads with insertion length =400bp, and the standard deviation of the distance for pairs is 50bp which is default value. Because of simulated reads, I think they may be perfectly or hi ...
written 2.1 years ago by jesselee516100
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bowtie2 paired end insertion length
... Hi, I am using bowtie2 to do alignment to reference genome. Actually, instead of getting real data, I simulated the paired-end reads(100bp) with insertion length as 400bp between mate1 and mate2. Does anyone has any idea how to set the parameters for bowtie2 in this case? Because I simulated the re ...
bowtie2 ngs alignment paired end written 2.1 years ago by jesselee516100 • updated 2.1 years ago by d-cameron2.2k
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Answer: A: What are the examples of mixture of closely related bacterial strains?
... Hi, everyone. I am looking the paper you mentioned now. Do you have any idea which datasets are the 36 in vitro datasets said in the paper. I know I can get all dataset from [PRJEB1729][1]. But there are too many there. And Do you know how to get the real SNPs for the 36 in vitro datasets? [1]: ...
written 2.1 years ago by jesselee516100
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Comment: C: Where to find archived NCBI taxonomy file
... Ok. Thanks for your suggestion ...
written 2.2 years ago by jesselee516100
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Comment: C: Where to find archived NCBI taxonomy file
... Hi natasha, Thanks for help. Sorry for not clearly ask my question. I am actually the historical lineage information(should be names.dmp and node.dmp files), like when some phylum, class, order, family, genus and species added into the database. ...
written 2.2 years ago by jesselee516100

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