User: cecilio11

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cecilio1140
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Posts by cecilio11

<prev • 24 results • page 1 of 3 • next >
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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 6 days ago by cecilio1140 • updated 6 days ago by jrj.healey11k
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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 6 days ago by cecilio1140
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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 3 months ago by cecilio1140
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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 3 months ago by cecilio1140
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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 3 months ago by cecilio1140
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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 3 months ago by cecilio1140
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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 3 months ago by cecilio1140 • updated 3 months ago by Istvan Albert ♦♦ 80k
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Comment: C: Interpreting mapping contaminants
... I see. It may be better to sequence the bacteria again, making sure that there is no contamination. ...
written 3 months ago by cecilio1140
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Comment: C: Interpreting mapping contaminants
... h.mon, That sounds great. There are so many tools for cleaning contaminants. I wonder if I have closely related bacterial species, are those tools sensitive enough to distinguish between genes that have been horizontally transmitted between bacteria and are not in fact contaminants? Regards, Cecilio ...
written 4 months ago by cecilio1140
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Comment: C: Interpreting mapping contaminants
... WouterDeCoster, Thank you for your comment. I will apply your suggested "pipe" to my next alignments. What is your opinion on using the options "-G0" (no introns because these are bacteria) and "-N 5 --secondary=no" (no secondary alignments)? So, I would have to drop the option -x (setting multip ...
written 4 months ago by cecilio1140

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