User: Fabio Marroni
Fabio Marroni • 2.4k
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Posts by Fabio Marroni
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... I am afraid I cannot help then, I know nothing about WSL. ...
written 11 days ago by
Fabio Marroni • 2.4k
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... 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 Marroni • 2.4k
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... 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 Marroni • 2.4k
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... 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 Marroni • 2.4k
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... 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 Marroni • 2.4k
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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 Marroni • 2.4k
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... 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 Marroni • 2.4k
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... 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 Marroni • 2.4k
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... 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 Marroni • 2.4k
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143
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... 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 Marroni • 2.4k
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