Moderator: John
John ♦ 12k
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Posts by John
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C: BQSR: when it is applicable?
... 1. is difficult to answer, but essentially yes. It's not quite so straight forward, because first the tool builds rules for the entire data, and nothing based on genomic mapping location. It will not see a mismatch on chr1:5000 100 times and say "the quality scores of chr1:5000 need to be reduced", ...
written 20 months ago by
John ♦ 12k
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C: BQSR: when it is applicable?
... Sure, um, well it's to do with how BQSR works. Let's start at the beginning. Base quality scores are the sequencing machines guess at how likely it is to be wrong when base calling. It is important to realise that it's not how likely the machine is to be wrong, but a *guess* at how likely the machin ...
written 20 months ago by
John ♦ 12k
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C: BQSR: when it is applicable?
... Eek, you're right, i pulled the 13m number from the [NCBI's FAQ][1], but it hasn't been updated since 2008 -_-;
Regarding PHRED scores, you're right, this is on the assumption Illumina is producing probabilities of error that match reality. I've always known their process as having a 1:1000 error r ...
written 20 months ago by
John ♦ 12k
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... Can you run "`head my.fastq`" and "`tail my.fastq`" on your file and paste the results here? One should be able to make a fair guess based on that.
Strictly speaking however, it's not possible to be able to determine this in all situations. FASTQ is a terrible file format for metadata. ...
written 21 months ago by
John ♦ 12k
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C: BQSR: when it is applicable?
... I think the probability of that would be tiny. You'd have to essentially have more variations in the genome of the individual than the sequencing technology. But i can see where you're coming from - take for example [this quote][1] from the NIH about what SNPs are:
> SNPs occur normally througho ...
written 21 months ago by
John ♦ 12k
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... Type-2 Diabetes is a neato example of something that's a combination of both. ...
written 21 months ago by
John ♦ 12k
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... MAPQ scores are not meaningful because BAM is not meaningful - or rather, the field has yet to define the difference between read-alignments (what BAM officially stores) and fragment-alignments (what most aligners produce).
The issue goes far deeper than MAPQ scores, but if you want to read about M ...
written 21 months ago by
John ♦ 12k
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... The vast majority of what AWS offers is unrelated to bioinformatic analysis. I give lot of examples in the first two paragraphs of the above, like DNS, SSL, etc. These are features that businesses and SMCs will pay a premium for, because setting that stuff up on your own is a real hassle. I was also ...
written 23 months ago by
John ♦ 12k
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C: Declining quality of biostars
... I think you'd need to really dramatically change the way threads are ordered on the main page, not ordered by time posted or time since last activity, but by using an algorithm much like Facebook's to push to the top of the page threads the site wishes users to see - perhaps because they are logged ...
written 2.0 years ago by
John ♦ 12k
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