User: Fabio Marroni
Fabio Marroni • 2.5k
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Posts by Fabio Marroni
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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 2 days ago by
Fabio Marroni • 2.5k
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97
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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 4 days ago by
Fabio Marroni • 2.5k
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120
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... 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 Marroni • 2.5k
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... 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 Marroni • 2.5k
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483
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... I am afraid I cannot help then, I know nothing about WSL. ...
written 11 weeks ago by
Fabio Marroni • 2.5k
1
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483
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1
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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 weeks ago by
Fabio Marroni • 2.5k
1
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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 3 months ago by
Fabio Marroni • 2.5k
0
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201
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1
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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 3 months ago by
Fabio Marroni • 2.5k
0
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201
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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 3 months ago by
Fabio Marroni • 2.5k
1
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3.0k
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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 Marroni • 2.5k
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