User: Tom

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Tom20
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1 year, 10 months ago
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t****@ucdavis.edu

Posts by Tom

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Comment: C: How do I count the number of nucleotides using jellyfish; can I obtain the numbe
... Are Ns factored into jellyfish? Or are they just straight up ignored? ...
written 15 months ago by Tom20
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Comment: C: How do I count the number of nucleotides using jellyfish; can I obtain the numbe
... I believe the approximation is: total bases = (total-kmers-found) * readlength / (readlength - k - 1) If I'm not mistaken. I seem to be getting better results with this metric. I believe the -C option in jellyfish may play a role influencing this calculation ...
written 15 months ago by Tom20
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Comment: C: How do I count the number of nucleotides using jellyfish; can I obtain the numbe
... It could just not be possible to obtain this information doing de novo assembly and multiplying the assembly size by depht ...
written 15 months ago by Tom20
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Comment: C: How do I count the number of nucleotides using jellyfish; can I obtain the numbe
... Yeah no, that's just not working out for me. My read sizes are 251 and calculation is no where close to 121916338 ...
written 15 months ago by Tom20
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Comment: C: How do I count the number of nucleotides using jellyfish; can I obtain the numbe
... (These are raw reads not assemblies.) Think of the problem like this: Suppose you were ONLY given the .jf file. Derive how many nucleotides the original rawread file had. ...
written 15 months ago by Tom20
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Comment: C: How do I count the number of nucleotides using jellyfish; can I obtain the numbe
... I'm quantifying the amount of nucleotide information in my raw read, which seems like it should be straightforward. What I really want to know is whether or not there is a special setting or mathematical algorithm I would need to apply to obtain a number close to 121916338, based purely off of the . ...
written 15 months ago by Tom20
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How do I count the number of nucleotides using jellyfish; can I obtain the number of nucleotides that went into a mer_counts.jf from jellyfish stats?
... I have a comparison that's been puzzling me. Suppose I have a fastq file for a bacteria: rawread.fastq I do: `cat rawread.fastq | awk 'NR%4==2{print}' | tr -d '\n' | wc -c` to count the exact number of nucleotides in the rawread file. I get `121916338` ------ I proceed to do a jellyfish analysis: ...
k-mer kmer genomics jellyfish written 15 months ago by Tom20
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Comment: C: What are some drawbacks in using highly conserved genes to determine genomic com
... If not the person specifically; do you know of any papers that would illustrate this evidence? I'm unable to find anything ...
written 15 months ago by Tom20
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Comment: C: What are some drawbacks in using highly conserved genes to determine genomic com
... Do you have a name for this guy? ...
written 15 months ago by Tom20
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Comment: C: What are some drawbacks in using highly conserved genes to determine genomic com
... Thats a really cool observation, can I have a reference to what you're talking about? I'm doing a discussion on this topic and it would be most helpful! ...
written 16 months ago by Tom20

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