User: AP

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AP90
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Posts by AP

<prev • 41 results • page 1 of 5 • next >
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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 24 days ago by AP90
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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 7 months ago by AP90
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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 7 months ago by AP90
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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 7 months ago by AP90 • updated 7 months ago by genomax70k
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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 8 months ago by AP90
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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 8 months ago by AP90
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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 16 months ago by AP90
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Comment: C: Genome Assembly at low coverage?
... It is from animal data ...
written 16 months ago by AP90
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Comment: C: Genome Assembly at low coverage?
... Not really unfortunately. I won't have enough material for more cells. I have enough to get a coverage of about 8X. ...
written 17 months ago by AP90
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Comment: C: Genome Assembly at low coverage?
... Yes indeed, I am not planning on throwing the data away - although a new library would require a new individual. So not ideal to combine data from two different individuals. ...
written 17 months ago by AP90

Latest awards to AP

Popular Question 7 months ago, created a question with more than 1,000 views. For Empty VCF file with bcftools call
Scholar 8 months ago, created an answer that has been accepted. For A: Empty VCF file with bcftools call
Popular Question 16 months ago, created a question with more than 1,000 views. For Empty VCF file with bcftools call
Popular Question 16 months ago, created a question with more than 1,000 views. For Difference between bcftools view and bcftools call?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Empty VCF file with bcftools call
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Difference between bcftools view and bcftools call?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For vcftools does not filter by GQ
Scholar 3.3 years ago, created an answer that has been accepted. For A: Empty VCF file with bcftools call

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