User: rmf
rmf • 440
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Posts by rmf
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... For fast LD computation directly from a VCF file, see [here](https://www.biostars.org/p/347796/). ...
written 8 days ago by
rmf • 440
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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 8 days ago by
rmf • 440
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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 19 days ago by
rmf • 440
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... I think `wc -m` counts the newline characters as well. What we actually want is `total chars - newline chars = bases`. ...
written 4 weeks ago by
rmf • 440
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... Ah right! Ensembl count for human is based on the primary assembly. And some organisms don't have primary assemblies, just the top-level. ...
written 4 weeks ago by
rmf • 440
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... I am calculating the total genome length from a fasta file using the following code
`zcat genome.fa.gz | grep -v ">" | wc | awk '{print $3-$1}'`
For [Yeast](ftp://ftp.ensemblgenomes.org/pub/fungi/release-41/fasta/saccharomyces_cerevisiae/dna/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa.gz), ...
written 4 weeks ago by
rmf • 440
• updated
4 weeks ago by
Nicolas Rosewick ♦ 6.9k
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... Well.. Your error message says your input fastq file is not in gzip format. In that case you have to modify the script to accept non-gzipped fastq files. Change `zcat` to `cat`. That's as far as I can see. ...
written 5 weeks ago by
rmf • 440
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... I think VST counts from DESeq2 might be a good choice (seq depth+composition bias correction) for heatmaps and MDS. But I think VST is not controlling for gene length. I am not sure if it is possible to get length normalised VST. ...
written 5 weeks ago by
rmf • 440
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Comment:
C: Raw counts to TPM in R
... Cool! I get the same result.
# michael's version
# https://support.bioconductor.org/p/91218/
tpm3 <- function(counts,len) {
x <- counts/len
return(t(t(x)*1e6/colSums(x)))
}
Michael's version is much faster despite all the transposes.
![enter image description h ...
6
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... Can someone verify if this R code for converting raw counts to TPM is correct?
#' @title Compute TPM for a read count matrix
#' @param dfr A numeric data.frame of read counts with samples (columns) and genes (rows).
#' @param len A vector of gene cds length equal to number of rows of df ...
written 11 weeks ago by
rmf • 440
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