User: rmf
rmf • 550
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Posts by rmf
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... This is the code that I use in R.
#' @title get_mv
#' @description Compute M values from beta values
#' @param B A beta value matrix where rows are probes and columns are samples
#' @return Returns an M value matrix
#'
get_mv <- function(B)
{
if(missing(B)) st ...
written 8 days ago by
rmf • 550
0
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... Once you figure out what the different parts of your header mean, you can split them apart using regular expressions. ...
written 4 weeks ago by
rmf • 550
2
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158
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... I have a few bacterial whole genomes. I would like to alignment them to each other (multiple sequence alignment) and interactively explore the alignment/bases along with annotations. I have fasta genomes along with respective gff annotations. I am interested in knowing what are currently the best to ...
written 4 weeks ago by
rmf • 550
0
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... It keeps the fasta headers but seems to do some cleaning. In my case, commas (,) were converted to underscores (_). Turns out this can be turned off using ` -sformat pearson` (https://www.biostars.org/p/111857/). ...
written 4 weeks ago by
rmf • 550
1
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Answer:
A: PacBio merge runs
... I managed to get it to work. Not sure if this is the best way.
I converted `*.bax.h5` to BAM separately for each run.
bax2bam -o "sample1_run1" $(find . -name "*.bax.h5")
bax2bam -o "sample1_run2" $(find . -name "*.bax.h5")
This creates scraps and subreads BAM files. I merged the subread ...
written 3 months ago by
rmf • 550
1
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1
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... For one of my samples, I have two runs.
sample1
+-- run1/
| +-- *.bax.h5
+-- run2/
+-- *.bax.h5
My workflow involves using **bax2bam** to convert *.bax.h5* to *unaligned bam*. Then using **pbalign** to convert *unaligned bam* to *aligned bam*.
How do I combine these two ...
written 3 months ago by
rmf • 550
0
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2
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924
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2
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... How exactly does one use the XML file? At what point and where? ...
written 3 months ago by
rmf • 550
1
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3
answers
3.6k
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3
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... For fast LD computation directly from a VCF file, see [here](https://www.biostars.org/p/347796/). ...
written 4 months ago by
rmf • 550
7
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0
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572
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6 follow
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... Fast LD computation from a VCF file using **vcftools**, **bcftools** and **tomahawk**. Install **tomahawk** from [here](https://github.com/mklarqvist/tomahawk).
Following commands are run on the Linux command-line.
For LD computation, pairwise comparisons are performed between all SNPs, therefore ...
written 4 months ago by
rmf • 550
1
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3
answers
3.6k
views
3
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... You are right. I don't use it here. The `mid` variable is just used to find the mid point of the interval windows. When plotting, you could use `mid` instead of `start`. That was my plan, but then it turns out, it doesn't make much difference for this particular plot. ...
written 4 months ago by
rmf • 550
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