User: rmf

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rmf440
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Posts by rmf

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Comment: C: LD-decay in a r2 vs distance(cm) plot
... For fast LD computation directly from a VCF file, see [here](https://www.biostars.org/p/347796/). ...
written 8 days ago by rmf440
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Tutorial: Fast LD computation from VCF files using tomahawk
... 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 ...
bcftools ld vcf tutorial snp vcftools written 8 days ago by rmf440
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Comment: C: LD-decay in a r2 vs distance(cm) plot
... 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 rmf440
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Comment: C: Fasta length does not match Ensembl info
... 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 rmf440
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Comment: C: Fasta length does not match Ensembl info
... 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 rmf440
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Fasta length does not match Ensembl info
... 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), ...
fasta annotation written 4 weeks ago by rmf440 • updated 4 weeks ago by Nicolas Rosewick6.9k
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Comment: C: bwa mem: Passing a variable to read group
... 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 rmf440
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Comment: C: Data for drawing Heatmaps (RNA-seq)
... 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 rmf440
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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 ...
written 11 weeks ago by rmf440 • updated 10 weeks ago by RamRS19k
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Raw counts to TPM in R
... 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 ...
R rna-seq written 11 weeks ago by rmf440

Latest awards to rmf

Appreciated 17 days ago, created a post with more than 5 votes. For A: LD-decay in a r2 vs distance(cm) plot
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Design matrix not of full rank.
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Design matrix not of full rank.
Scholar 3 months ago, created an answer that has been accepted. For A: bowtie2-build cannot use multiple cores
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: LD-decay in a r2 vs distance(cm) plot
Popular Question 4 months ago, created a question with more than 1,000 views. For RNA-Seq experiment has low fold change
Popular Question 6 months ago, created a question with more than 1,000 views. For RNA-Seq experiment has low fold change
Popular Question 6 months ago, created a question with more than 1,000 views. For Design matrix not of full rank.
Centurion 6 months ago, created 100 posts.
Scholar 6 months ago, created an answer that has been accepted. For A: bowtie2-build cannot use multiple cores
Appreciated 8 months ago, created a post with more than 5 votes. For A: LD-decay in a r2 vs distance(cm) plot
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: LD-decay in a r2 vs distance(cm) plot
Popular Question 8 months ago, created a question with more than 1,000 views. For Design matrix not of full rank.
Scholar 8 months ago, created an answer that has been accepted. For A: bowtie2-build cannot use multiple cores
Scholar 8 months ago, created an answer that has been accepted. For A: Regenotype vcf using some samples as reference
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: LD-decay in a r2 vs distance(cm) plot
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: LD-decay in a r2 vs distance(cm) plot
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Popular Question 14 months ago, created a question with more than 1,000 views. For Design matrix not of full rank.
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Popular Question 24 months ago, created a question with more than 1,000 views. For RNA Seq: GC Content extra peak
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Scholar 2.0 years ago, created an answer that has been accepted. For A: bowtie2-build cannot use multiple cores
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