User: Fabio Marroni
Fabio Marroni • 2.5k
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Posts by Fabio Marroni
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C: Why sortmerna 4.2.0 runs so slow?
... I would either try another installation (source code or conda), or ask authors for help. The behavior is strange indeed. ...
written 6 weeks ago by
Fabio Marroni • 2.5k
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Comment:
C: Why sortmerna 4.2.0 runs so slow?
... Wow, I didn't even know about 4.2.0. I followed the link on the paper and got version 2.1. Just out of curiosity, are you using the binaries or you compiled from source code? I don't know if this could affect (it shouldn't but you never know). ...
written 6 weeks ago by
Fabio Marroni • 2.5k
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... Hi!
First of all, we cannot see the picture. Maybe you want to read this post on [how to post figures on Biostars][1].
Then, if the question is how to download the eqtl data from GTEx the answer is:
Go to [GTEx page][2], select the dataset you want and download it.
While for some datasets you would ...
written 9 weeks ago by
Fabio Marroni • 2.5k
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... You can give a look to [this related post][1]
[1]: https://www.biostars.org/p/364108/ ...
written 3 months ago by
Fabio Marroni • 2.5k
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... If you don't have a spike-in of known concentration is impossible. See answers to a similar question [here][1]
[1]: https://www.biostars.org/p/8991/ ...
written 3 months ago by
Fabio Marroni • 2.5k
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... If P(Ab)=P(aB)=0, then, by definition P(A)=P(B) and p(a)=p(b) because alleles A and B are only found in the AB haplotype, and a and b alleles are only found in the ab haplotype.
Thus -P(A)P(b)] / [sqrt((P(A)P(B)(P(a)P(b))]
becomes
-P(A)P(a)/ [sqrt((P(A)P(A)(P(a)P(a))]
i.e.
-P(A)P(a)/[sqrt(( ...
written 3 months ago by
Fabio Marroni • 2.5k
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... You can give a look to [this][1] post
[1]: https://www.biostars.org/p/87222/ ...
written 3 months ago by
Fabio Marroni • 2.5k
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... In addition (and sorry if I revive a zombie-post), I ***think*** that the correct way to perform the analysis with ballgown would be to set `libadjust` to FALSE, otherwise you will get FPKM (which already normalize somehow for the success of a sequencing run) that are then scaled as (quoting the man ...
written 3 months ago by
Fabio Marroni • 2.5k
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... Mmmm, it looks like the entire chromosome contains only one SNP. Is it correct? Maybe Beagle is not ready to deal with chromosomes/regions with only one SNP. Maybe this is the issue?
BTW, it looks like the link to the warning message is broken.
...
written 3 months ago by
Fabio Marroni • 2.5k
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219
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... The window in which beagle gets stucked is only one bp long, while others are several kb.
Can you give a look at the input file in the position in which beagle gets stucked? Maybe there is something strange there... ...
written 3 months ago by
Fabio Marroni • 2.5k
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