User: Fabio Marroni

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Fabio Marroni2.5k
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Posts by Fabio Marroni

<prev • 407 results • page 1 of 41 • next >
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Comment: 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 Marroni2.5k
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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 Marroni2.5k
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Answer: A: Reproduction eQTL GTex Box plot
... 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 Marroni2.5k
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Answer: C: How to extract coverage of custom target regions (bed file) from a bam file?
... You can give a look to [this related post][1] [1]: https://www.biostars.org/p/364108/ ...
written 3 months ago by Fabio Marroni2.5k
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Comment: C: How to covert RKPM into absolute quantification?
... 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 Marroni2.5k
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Answer: A: Question about the correlation coefficient for Linkage Disequilibrium (LD)
... 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 Marroni2.5k
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Answer: A: Adjusting the Fst values for different sample sizes
... You can give a look to [this][1] post [1]: https://www.biostars.org/p/87222/ ...
written 3 months ago by Fabio Marroni2.5k
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Comment: C: Ballgown finds few DE genes compared to DESeq
... 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 Marroni2.5k
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Comment: C: The genotype imputation in Beagle always stop on specific step and can not finis
... 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 Marroni2.5k
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Comment: C: The genotype imputation in Beagle always stop on specific step and can not finis
... 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 Marroni2.5k

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Popular Question 11 weeks ago, created a question with more than 1,000 views. For topGO is performing enrichment test on GO terms that are not present in my dataset
Scholar 11 months ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
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Teacher 13 months ago, created an answer with at least 3 up-votes. For A: What Is Ivsi Number Of A Mutation?
Scholar 17 months ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: What Is Ivsi Number Of A Mutation?
Scholar 18 months ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Good Answer 19 months ago, created an answer that was upvoted at least 5 times. For A: Sample Sam File
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: What Is Ivsi Number Of A Mutation?
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Scholar 2.6 years ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Appreciated 2.6 years ago, created a post with more than 5 votes. For A: What Is Ivsi Number Of A Mutation?
Commentator 2.6 years ago, created a comment with at least 3 up-votes. For C: error in R
Scholar 2.7 years ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Scholar 2.7 years ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
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Scholar 2.9 years ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?

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