User: ctseto

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ctseto250
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Posts by ctseto

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Comment: C: kraken2 different bacteria read counts on custom database
... My interpretation here is that db two without human classifies human as "0" (unclassified. It seems it is 131567 /or/ 1280, depending on the database; at least for Read1 In read2 it is either 9606 or 2759, in your database sans human 0 or 1280. In read 2 the first 21 kmers are human; without human ...
written 25 days ago by ctseto250
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Comment: C: How to determine species of paired-end .fastq files (low mapping rates and incon
... I'm guessing Kraken1, as you mention bacteria | virus | plasmid, which I vaguely remember are the databases used in Kraken1. ...
written 27 days ago by ctseto250
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Comment: C: How to determine species of paired-end .fastq files (low mapping rates and incon
... A complex path could easily be a tangly genome with lots of recombination or multiple related strains, and teasing those apart with just paired end is tricky; but you can still generate draft genomes and try to annotate. It would be tempting to just focus on the Helicobacters, but the "unknowns" ar ...
written 28 days ago by ctseto250
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Comment: C: How to determine species of paired-end .fastq files (low mapping rates and incon
... I would not describe Metaphlan2 as a tool suited for eukaryotes. Kraken2 is just a kmer lookup database, and the fact that you need to use separate databases makes me think you'd be better off running this in command line as well, perhaps after all the other jobs. It doesn't use too much memory, but ...
written 28 days ago by ctseto250
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Comment: C: How to determine species of paired-end .fastq files (low mapping rates and incon
... It's a sam flag: https://broadinstitute.github.io/picard/explain-flags.html read paired (0x1) read unmapped (0x4) mate unmapped (0x8) is 13. You add 64 and 128 to 13 for your flags if you want to specifically pull read one or read 2. In this case you map reads to dolphin and you want ...
written 28 days ago by ctseto250
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Comment: C: How to determine species of paired-end .fastq files (low mapping rates and incon
... You could probably try mapping reads to a host genome. I see that Baylor HGSC was working on a dolphin genome project, though I'm not sure how confident I am in it, and estimate based on PE read numbers. Then you passthrough all the reads that did not map (if memory serves, f13 + f64/f128 for read ...
written 4 weeks ago by ctseto250
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Comment: C: How to determine species of paired-end .fastq files (low mapping rates and incon
... In re Kraken; consider alternate databases (this will require local deployment) https://lomanlab.github.io/mockcommunity/mc_databases.html ...
written 4 weeks ago by ctseto250
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Comment: C: How to determine species of paired-end .fastq files (low mapping rates and incon
... 2. We're not saying that there isn't Helico, but fixating prematurely on "all map well to Helico" when it may not all be 100% Helico (or even a single strain of Helico!) could be a problem. One possibility is multiple strains of helico that got stitched together, which from Metaphlan, might not be ...
written 4 weeks ago by ctseto250
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Comment: C: How to determine species of paired-end .fastq files (low mapping rates and incon
... Metaphlan estimates from species specific markers, which is probably better at relating back to relative abundance. As for Kraken, its percentages are % of contigs (omitting PE reads and coverage per contig), so they are different measures of abundance. ...
written 4 weeks ago by ctseto250
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Comment: C: How to determine species of paired-end .fastq files (low mapping rates and incon
... disregard this post, superfluous. ...
written 4 weeks ago by ctseto250

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