User: cecilio11

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cecilio1150
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Posts by cecilio11

<prev • 27 results • page 1 of 3 • next >
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Has anyone used the DNALink sequencing service for sequencing genomes?
... Hello all, I am planning to send the DNA of two bacteria to be sequenced at DNALink (http://www.dnalink.com/english/). The sequencing facility is located in South Korea and they have offices in California. They have quoted a good price for sequencing the two bacteria by using the PacBio RS II SMRT ...
next-gen written 11 weeks ago by cecilio1150
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Comment: C: illumina sequencing reads with high quality scores have low percentage mapping t
... >Ignatzschineria larvae I assume that is the actual name of the bacterium. Word larvae just happens to be a species name? > Yes sir, a funny and confusing specific epithet for a bacterial species, right? "larvae". > I assume this experiment is referring to a pure colony of a bacteriu ...
written 3 months ago by cecilio1150
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illumina sequencing reads with high quality scores have low percentage mapping to refseq and classification?
... Hello Biostars, I am assembling my first illumina genome. It is a bacterial genome about 2.5 MB in size. genus Ignatzschineria. FastQC shows the following stats for the R1 and R2 reads: File type-----------------------------Conventional base calls Encoding----------------------------Sanger / Ill ...
genome sequencing written 3 months ago by cecilio1150
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aligning reads varying from 110bp to 56520bp to a reference sequence
... Hi Biostars, I have a set of sequences (from a genome sequencing file) that mapped to a reference sequence (let's name it "ref1"). The file containing the mapped sequences could be named "mapped_ref1". The sizes of those sequences vary from 110bp to 56520bp. Those sequences do not represent the who ...
alignment written 5 months ago by cecilio1150 • updated 3 months ago by Biostar ♦♦ 20
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Answer: A: Kraken2 vs Minimap2 and Blast results seem to be incongruent
... I posted this issue a while ago. I was starting my work on genomics those days. I am nostalgic of those times, three months ago. I found out that the reason for the no congruent results between mapping by minimap2 and classifying by Kraken2 was that the database of the latter did not contain the ge ...
written 5 months ago by cecilio1150
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Comment: C: Kraken2 vs Minimap2 and Blast results seem to be incongruent
... h.mom and colindaven, Thank you for your answer. For the raw reads, I did run Minimap2 and kraken2 in an IBM cluster. And yes, I run Minimap2 with a single reference sequence per run per bacteria. The percentages refer to each single run. For the draft assemblies, I run Blast (bacterial genomes an ...
written 8 months ago by cecilio1150
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Comment: A: Kraken2 vs Minimap2 and Blast results seem to be incongruent
... h.mom and colindaven, Thank you for your answer. See below. ...
written 8 months ago by cecilio1150
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Kraken2 vs Minimap2 and Blast results seem to be incongruent
... Hello, I obtained incongruent "classification" results when running Kraken2 vs. Minimap2 and Blast on the same data sets. I am planning to assemble 5 bacterial genomes from pacbio reads. For 2 of the bacteria I generated two raw assemblies by using Canu. I suspected that there may be some contamin ...
genome assembly written 8 months ago by cecilio1150
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Are these Canu genome assemby setings appropriate for bacteria?
... Hi, I am trying to assemble bacterial genomes from pacbio reads. I am using CANU. ISSUES I FOUND: I run into some issues with the draft assemblies, such as the presence of some "undesired DNA" in the reads, and the blast searches show that the draft assemblies do not match well to the reference s ...
assembly written 8 months ago by cecilio1150
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Are these good parameters for bacterial genome assembly?
... Hi, I am trying to assemble bacterial genomes from pacbio reads. I am suing CANU. ISSUES I FOUND: I run into some issues with the draft assemblies, such as the presence of some "undesired DNA" in the reads, and the blast searches show that the draft assemblies do not match well to the reference s ...
assembly written 8 months ago by cecilio1150 • updated 8 months ago by Istvan Albert ♦♦ 81k

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