User: Tom

Tom20
Reputation:
20
Status:
New User
Location:
United States
Last seen:
2 years, 11 months ago
Joined:
3 years, 8 months ago
Email:
t****@ucdavis.edu

Posts by Tom

<prev • 38 results • page 1 of 4 • next >
1
1.3k
views
1
... Are Ns factored into jellyfish? Or are they just straight up ignored? ...
written 3.1 years ago by Tom20
1
1.3k
views
1
... 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 3.1 years ago by Tom20
1
1.3k
views
1
... It could just not be possible to obtain this information doing de novo assembly and multiplying the assembly size by depht ...
written 3.1 years ago by Tom20
1
1.3k
views
1
... Yeah no, that's just not working out for me. My read sizes are 251 and calculation is no where close to 121916338 ...
written 3.1 years ago by Tom20
1
1.3k
views
1
... (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 3.1 years ago by Tom20
1
1.3k
views
1
... 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 3.1 years ago by Tom20
1
1.3k
views
1
... 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: ...
written 3.1 years ago by Tom20
1
950
views
1
... If not the person specifically; do you know of any papers that would illustrate this evidence? I'm unable to find anything ...
written 3.1 years ago by Tom20
1
950
views
1
... Do you have a name for this guy? ...
written 3.1 years ago by Tom20
1
950
views
1
... 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 3.2 years ago by Tom20

Latest awards to Tom

No awards yet. Soon to come :-)

Content
Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.