User: AP

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AP100
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Posts by AP

<prev • 44 results • page 1 of 5 • next >
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Comment: C: Oxford Nanopore and Coverage
... Thank you very much, this is quite useful. I haven't used NanoPlot but will take a look. ...
written 7 months ago by AP100
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Comment: C: Oxford Nanopore and Coverage
... Yes absolutely. But I was hoping to be able to have a rough estimate without using a bioinformatics pipeline (similar to what can be done with Illumina technology). ...
written 7 months ago by AP100
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Oxford Nanopore and Coverage
... Hello, I was wondering if anyone knew how to calculate the coverage of a specific genome using output metrics from Oxford Nanopore Technology. For instance, can anyone calculate coverage information using the total number of pores ran, the N50, and the data in Gb? Information of the expected geno ...
coverage oxford nanopore written 7 months ago by AP100
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Answer: A: Genetic PCA from poolseq genotype file
... Hi Natalia, Yes, I did manage to run a PCA using the sync file. The way I did it was to first calculate the frequency of the minor allele (or the major) of all the SNPs. Then, I ran a PCA on R using prcomp. Instead of the frequency, you can also just use the total count of the minor or major allele ...
written 14 months ago by AP100
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Comment: C: Number of passing clusters vs. number of read pairs vs. total number of reads
... Thanks but I don't find it very helpful and clear. I like being able to calculate this by hand myself. ...
written 20 months ago by AP100
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Comment: C: Number of passing clusters vs. number of read pairs vs. total number of reads
... OK thank you very much for the clarification! So, does that mean I should consider 300M reads when calculating the number of lanes required for e.g. a 20X coverage (like in the example above?); Or should I double the number of reads? ...
written 20 months ago by AP100
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Number of passing clusters vs. number of read pairs vs. total number of reads
... Hi all, I apologize for a rather basic question but I am confused about the terminology. What is really the difference between: - Number of passing filters - Number of clusters - Number of read pairs per lane - Total number of reads For instance, Hiseq 4000 should produce about 300M reads per l ...
reads illumina flowcell written 20 months ago by AP100 • updated 20 months ago by genomax90k
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Answer: A: Correct Interval Coverage data for overall number of raw reads
... Two ways of doing it: 1. Downsizing: can be done using samb: http://lomereiter.github.io/sambamba/ 2. Normalise the data to a mean of zero and sd of 1 I guess I answered my own question... :) ...
written 22 months ago by AP100
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Correct Interval Coverage data for overall number of raw reads
... Hello, I have two datasets with Interval Coverage metrics that I would like to compare. However, both datasets have a significant different amount of raw reads. I would like to normalise or correct for this different amount of raw reads in order to make the interval data coverage comparable. Any ...
sequencing written 22 months ago by AP100
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Genetic PCA from poolseq genotype file
... Hello, I have a sync file extracted with Popoolation2 software that looks like that: Contig Position Ref Pool1 Pool2 Pool3 Pool4 SCAFOLD1 11722 A 330:0:0:0:0:0 315:0:0:0:0:0 334:0:0:0:0:0 111:0:0:0:0:0 SCAFOLD1 11723 T 0:330:0:0:0:0 0:316:0:0:0:0 0:334:0:0:0:0 ...
pca poolseq genotype popoolation written 2.5 years ago by AP100 • updated 12 months ago by ndiaz0

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Popular Question 2.5 years ago, created a question with more than 1,000 views. For Difference between bcftools view and bcftools call?
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Scholar 4.4 years ago, created an answer that has been accepted. For A: Empty VCF file with bcftools call

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