User: rmf

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rmf550
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Posts by rmf

<prev • 127 results • page 1 of 13 • next >
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Answer: A: M Value from Non-Normalized Methylated and Unmethylated Signal 450k
... 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 rmf550
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Comment: C: bwa mem: Passing a variable to read group
... 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 rmf550
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Multiple sequence alignment and visualisation for bacterial genomes
... 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 ...
genome bacteria alignment msa sequencing written 4 weeks ago by rmf550
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Comment: C: Command line tool for translated multifasta nucleotide to aminoacid sequence
... 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 rmf550
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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 rmf550
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PacBio merge runs
... 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 ...
assembly pacbio written 3 months ago by rmf550
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Comment: C: Arrow Assembly polishing Error "KeyError: 'BASECALLERVERSION'"
... How exactly does one use the XML file? At what point and where? ...
written 3 months ago by rmf550
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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 4 months ago by rmf550
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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 4 months ago by rmf550
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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 4 months ago by rmf550

Latest awards to rmf

Popular Question 8 weeks ago, created a question with more than 1,000 views. For Design matrix not of full rank.
Student 8 weeks ago, asked a question with at least 3 up-votes. For RNASeq: Differential gene expression and qqplot
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Design matrix not of full rank.
Scholar 12 weeks ago, created an answer that has been accepted. For A: bowtie2-build cannot use multiple cores
Appreciated 3 months ago, created a post with more than 5 votes. For A: LD-decay in a r2 vs distance(cm) plot
Popular Question 3 months ago, created a question with more than 1,000 views. For Design matrix not of full rank.
Appreciated 4 months ago, created a post with more than 5 votes. For A: LD-decay in a r2 vs distance(cm) plot
Popular Question 5 months ago, created a question with more than 1,000 views. For Design matrix not of full rank.
Popular Question 6 months ago, created a question with more than 1,000 views. For Design matrix not of full rank.
Scholar 7 months ago, created an answer that has been accepted. For A: bowtie2-build cannot use multiple cores
Teacher 7 months ago, created an answer with at least 3 up-votes. 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 RNA-Seq experiment has low fold change
Popular Question 10 months ago, created a question with more than 1,000 views. For RNA-Seq experiment has low fold change
Popular Question 10 months ago, created a question with more than 1,000 views. For Design matrix not of full rank.
Centurion 11 months ago, created 100 posts.
Scholar 11 months ago, created an answer that has been accepted. For A: bowtie2-build cannot use multiple cores
Appreciated 12 months ago, created a post with more than 5 votes. For A: LD-decay in a r2 vs distance(cm) plot
Good Answer 12 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 13 months ago, created a question with more than 1,000 views. For Design matrix not of full rank.
Scholar 13 months ago, created an answer that has been accepted. For A: bowtie2-build cannot use multiple cores
Scholar 13 months ago, created an answer that has been accepted. For A: Regenotype vcf using some samples as reference
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: LD-decay in a r2 vs distance(cm) plot
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: LD-decay in a r2 vs distance(cm) plot
Scholar 13 months ago, created an answer that has been accepted. For A: bowtie2-build cannot use multiple cores
Voter 15 months ago, voted more than 100 times.

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