User: cecilio11

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cecilio1130
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Posts by cecilio11

<prev • 22 results • page 1 of 3 • next >
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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 days ago by cecilio1130
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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 days ago by cecilio1130
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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 9 days ago by cecilio1130
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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 22 days ago by cecilio1130
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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 22 days ago by cecilio1130 • updated 18 days ago by Istvan Albert ♦♦ 78k
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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 22 days ago by cecilio1130
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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 weeks ago by cecilio1130
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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 weeks ago by cecilio1130
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Comment: C: Interpreting mapping contaminants
... WoterDeCoster and h.mon, I am running minimap2 in a cluster that use an LSF. The alignment output is written to a directory. The stdout is an empty file (because the .sam file is written to the directory). The stderr looks like this: [M::mm_idx_gen::0.150*0.78] collected minimizers [M::mm_idx_gen: ...
written 4 weeks ago by cecilio1130
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Interpreting mapping contaminants
... Dear Biostars, I am posting this question in this forum because I found this wonderful site is populated mostly by very kind and helpful people I am a beginner on the field of bioinformatics and genome assembly. I am working on assembling several bacterial genomes. The sequences were obtained fro ...
alignment written 5 weeks ago by cecilio1130 • updated 4 weeks ago by h.mon22k

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