User: Fabio Marroni

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Fabio Marroni2.5k
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Italy
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http://www.fabiomarron...
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14 hours ago
Joined:
8 years, 8 months ago
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Posts by Fabio Marroni

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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 2 days 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 4 days ago by Fabio Marroni2.5k
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Comment: C: issues using Value Matching command in R
... tab[tab[,1]=="ENSG00000223972.4",] You have to check that the first column is of character type. I also post the link to a [similar question on SO][1], where you can get further help. [1]: https://stackoverflow.com/questions/28261719/r-extracting-values-from-column-under-given-conditions-of ...
written 29 days ago by Fabio Marroni2.5k
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Comment: C: STAR ALIGNMENT: FATAL ERROR in reads input: short read sequence line: 0
... Did you give a look at the sequence of the read `@SRR6657766.4132571`? Maybe this would give an hint ...
written 4 weeks ago by Fabio Marroni2.5k
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Comment: C: Error message running admixture in WSL (Ubuntu) : Segmentation fault (core dumpe
... I am afraid I cannot help then, I know nothing about WSL. ...
written 11 weeks ago by Fabio Marroni2.5k
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Comment: C: Error message running admixture in WSL (Ubuntu) : Segmentation fault (core dumpe
... 1) did anybody try to inspect the memory usage as suggested by [i.sudbery][1]? What was the result? 2) did anybody try to run the same command on a reduced dataset? What was the result? 3) Admixture comes with a toy dataset (http://software.genetics.ucla.edu/admixture/download.html). Did anybody try ...
written 11 weeks ago by Fabio Marroni2.5k
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Comment: C: Beta coefficient is positive, but potential SNP effect size is negative
... The effect size is negative if the allele that is called "effect allele" confers a decrease in the measuread phenotype, and positive if it confers an increase. It is possible that in the regression the effect is calculated for allele A and then in the results the effect size is reported for allele B ...
written 3 months ago by Fabio Marroni2.5k
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Comment: C: Limma/edgeR or other for metagenomic (non-RNA) data?
... Sorry, not yet (only single time-point). I will do it shortly, and post developments if I find something that might be of help. ...
written 3 months ago by Fabio Marroni2.5k
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Answer: A: Limma/edgeR or other for metagenomic (non-RNA) data?
... I suggest you use the fitZig algorithm in [metagenomeSeq][1] package, which has been developed esplicitly for this, and that always gave me good results. [1]: https://bioconductor.org/packages/release/bioc/html/metagenomeSeq.html ...
written 3 months ago by Fabio Marroni2.5k
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Comment: C: HISAT2 MAPQ scoring scheme
... Although I followed this approach for several time, I realized that it is not the best one. I found at least one instance in which these fields provide wrong results Here the results I got with hisat2 reference --no-unal -1 small_LM3_R1.fastq -2 small_LM3_R2.fastq -S small_LM3.sam HWI ...
written 3 months ago by Fabio Marroni2.5k

Latest awards to Fabio Marroni

Scholar 7 months ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Scholar 9 months ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: What Is Ivsi Number Of A Mutation?
Scholar 13 months ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: What Is Ivsi Number Of A Mutation?
Scholar 15 months ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: Sample Sam File
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: What Is Ivsi Number Of A Mutation?
Appreciated 22 months ago, created a post with more than 5 votes. For A: What Is Ivsi Number Of A Mutation?
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: What Is Ivsi Number Of A Mutation?
Scholar 2.3 years ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Appreciated 2.3 years ago, created a post with more than 5 votes. For A: What Is Ivsi Number Of A Mutation?
Commentator 2.3 years ago, created a comment with at least 3 up-votes. For C: error in R
Scholar 2.4 years ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Scholar 2.4 years ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: What Is Ivsi Number Of A Mutation?
Scholar 2.5 years ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Teacher 2.6 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?
Scholar 3.3 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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