User: rmf

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rmf690
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Posts by rmf

<prev • 132 results • page 1 of 14 • next >
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Comment: C: Fixing batch effect with seurat integrate
... I also had the feeling something is wrong. Then, I have looked into it and I don't see anything obviously wrong. So, in the first plot, I use *nFeatures_RNA*, In the second plot, I manually recalculate *num of genes detected* from 'integrated' assay using `colSums(GetAssayData(su,assay="integrated") ...
written 2 days ago by rmf690
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Fixing batch effect with seurat integrate
... I have three 10X runs. If I merge them with `CreateSeuratObject()`, this is the distribution of genes detected for each run (batch) (nFeatures_RNA). ![enter image description here][1] If I integrate them, using hvg approach or sctransform approach. (Showing sctransform based integration below) ...
single-cell seurat scrna.seq written 3 days ago by rmf690
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Answer: C: UMAP interpretation in scRNA-seq analysis
... tSNE separates groups quite well, but does not preserve the global structure very well, therefore you cannot take three points and say two are closer than the other two. It does not preserve distance. Local structures may make sense. Therefore, it most likely doesn't show cell differentiation trajec ...
written 10 weeks ago by rmf690
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Applications of TPM normalisation
... I use raw counts for DGE in DESeq2, edgeR etc. And I use VST for PCA and clustering. Now, I am curious about TPM. What are the applications of a TPM normalised count table? What can it be used for? What are the drawbacks of TPM normalised counts? ![enter image description here][1] ![enter image de ...
deseq2 rna-seq normalisation dge written 10 weeks ago by rmf690
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Model selection for differential expression
... I am using limma to test for differential expression. And I am trying to find the best model to use. My variable of interest is **condition**. I have several batch variables **plate**, **well** and **gender** which seems to be highly associated with top three principal components in a PCA. I have f ...
methylation limma rna-seq differential expression written 3 months ago by rmf690
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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 4 months ago by rmf690
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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 5 months ago by rmf690
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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 5 months ago by rmf690
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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 5 months ago by rmf690
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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 7 months ago by rmf690

Latest awards to rmf

Popular Question 7 weeks ago, created a question with more than 1,000 views. For Gene length correction for dge
Popular Question 7 weeks ago, created a question with more than 1,000 views. For RNA Seq: GC Content extra peak
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Read count correlation between samples
Popular Question 7 weeks ago, created a question with more than 1,000 views. For RNA Seq: Differential expression model formula
Popular Question 7 weeks ago, created a question with more than 1,000 views. For gff3validator: gff3 validation error
Popular Question 10 weeks ago, created a question with more than 1,000 views. For RNA Seq: Differential expression model formula
Popular Question 3 months ago, created a question with more than 1,000 views. For RNA Seq: Differential expression model formula
Popular Question 3 months ago, created a question with more than 1,000 views. For What minimum read length to retain in a standard rna-seq dataset?
Popular Question 4 months ago, created a question with more than 1,000 views. For What minimum read length to retain in a standard rna-seq dataset?
Popular Question 6 months ago, created a question with more than 1,000 views. For Design matrix not of full rank.
Student 6 months ago, asked a question with at least 3 up-votes. For RNASeq: Differential gene expression and qqplot
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
Appreciated 7 months ago, created a post with more than 5 votes. For A: LD-decay in a r2 vs distance(cm) plot
Popular Question 7 months ago, created a question with more than 1,000 views. For Design matrix not of full rank.
Appreciated 8 months ago, created a post with more than 5 votes. For A: LD-decay in a r2 vs distance(cm) plot
Popular Question 9 months ago, created a question with more than 1,000 views. For Design matrix not of full rank.
Popular Question 10 months ago, created a question with more than 1,000 views. For Design matrix not of full rank.
Scholar 11 months ago, created an answer that has been accepted. For A: bowtie2-build cannot use multiple cores
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: LD-decay in a r2 vs distance(cm) plot
Popular Question 12 months ago, created a question with more than 1,000 views. For RNA-Seq experiment has low fold change
Popular Question 14 months ago, created a question with more than 1,000 views. For RNA-Seq experiment has low fold change
Popular Question 14 months ago, created a question with more than 1,000 views. For Design matrix not of full rank.
Centurion 15 months ago, created 100 posts.
Scholar 15 months ago, created an answer that has been accepted. For A: bowtie2-build cannot use multiple cores

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