User: Fabio Marroni

gravatar for Fabio Marroni
Fabio Marroni2.4k
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Italy
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http://www.fabiomarron...
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7 hours ago
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8 years, 6 months ago
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Posts by Fabio Marroni

<prev • 395 results • page 1 of 40 • next >
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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 days ago by Fabio Marroni2.4k
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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 days ago by Fabio Marroni2.4k
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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 4 weeks ago by Fabio Marroni2.4k
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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 5 weeks ago by Fabio Marroni2.4k
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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 5 weeks ago by Fabio Marroni2.4k
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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 6 weeks ago by Fabio Marroni2.4k
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Comment: C: Can primers for PCR be duplicated?
... Crossposted on seqanswers: http://seqanswers.com/forums/showthread.php?t=91115 Also, the question is not bioinformatics related, so it is a bit off-topic for biostars, and you are unlikely to get help here. You can read guides on how to post good questions (and maximize your chance of getting help) ...
written 10 weeks ago by Fabio Marroni2.4k
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Comment: C: Merging two files based on a particular column
... You merge your file 1 with the file 2 obtained as [i.sudbery][1] suggested and you get what you want (merge by default discard non-matching rows) [1]: https://www.biostars.org/u/16790/ ...
written 10 weeks ago by Fabio Marroni2.4k
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Comment: C: Merging two files based on a particular column
... Maybe you should use the grep function of R to simply grep the gene symbol of file 1 to that in file 2 and if the grep is not null you paste the colums to that row. You will need a loop, probably (or maybe a clever use of apply). ...
written 10 weeks ago by Fabio Marroni2.4k
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Comment: C: Plink: Fisher's Exact test ERROR: FEXACT error 3
... It is a problem probably related to the size of the matrix you are testing. One option would be to see if you can perform separate tests on subsets of your data. This would also rule out the hypothesis of malformed input. One option could be using a newer version of plink, since apparently they aba ...
written 12 weeks ago by Fabio Marroni2.4k

Latest awards to Fabio Marroni

Scholar 5 months ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Scholar 7 months ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: What Is Ivsi Number Of A Mutation?
Scholar 11 months ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: What Is Ivsi Number Of A Mutation?
Scholar 12 months ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Good Answer 13 months ago, created an answer that was upvoted at least 5 times. For A: Sample Sam File
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: What Is Ivsi Number Of A Mutation?
Appreciated 20 months ago, created a post with more than 5 votes. For A: What Is Ivsi Number Of A Mutation?
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: What Is Ivsi Number Of A Mutation?
Scholar 2.1 years ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Appreciated 2.1 years ago, created a post with more than 5 votes. For A: What Is Ivsi Number Of A Mutation?
Commentator 2.1 years ago, created a comment with at least 3 up-votes. For C: error in R
Scholar 2.2 years ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Scholar 2.2 years ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: What Is Ivsi Number Of A Mutation?
Scholar 2.4 years ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Teacher 2.4 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 2.4 years ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Scholar 3.1 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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