User: rmf

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rmf750
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Posts by rmf

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Variant calling pacbio bacteria
... I have PacBio reads from three bacterial genomes as three samples. They were de-novo assembled using HGAP4 and polished. One of samples was taken as reference. And subreads from each sample was mapped back to this reference for variant calling. Variant calling was performed using two workflows: ...
variant-calling sniffles bacteria pacbio pbsv written 3 months ago by rmf750 • updated 7 weeks ago by wrowell0
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Converting bax.h5 to CCS reads
... I have some pacbio reads. That's really the only info I have. No version number or anything. Each sample has four bax.h5 and one bas.h5. Is it possible to convert this to consensus reads? I tried running the `css` tool from `pbcss`. It runs but I get the report below: ZMW Yield Success (wi ...
pacbio written 3 months ago by rmf750
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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 3 months ago by rmf750
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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 months ago by rmf750
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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 6 months ago by rmf750
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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 6 months ago by rmf750
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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 7 months ago by rmf750
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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 months ago by rmf750
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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 8 months ago by rmf750
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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 8 months ago by rmf750

Latest awards to rmf

Popular Question 10 weeks ago, created a question with more than 1,000 views. For Gene length correction for dge
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Similarity between two FASTA files
Student 10 weeks ago, asked a question with at least 3 up-votes. For RNASeq: Differential gene expression and qqplot
Popular Question 3 months ago, created a question with more than 1,000 views. For Gene length correction for dge
Popular Question 5 months ago, created a question with more than 1,000 views. For Gene length correction for dge
Popular Question 5 months ago, created a question with more than 1,000 views. For RNA Seq: GC Content extra peak
Popular Question 5 months ago, created a question with more than 1,000 views. For Read count correlation between samples
Popular Question 5 months ago, created a question with more than 1,000 views. For RNA Seq: Differential expression model formula
Popular Question 5 months ago, created a question with more than 1,000 views. For gff3validator: gff3 validation error
Popular Question 6 months ago, created a question with more than 1,000 views. For RNA Seq: Differential expression model formula
Popular Question 6 months ago, created a question with more than 1,000 views. For RNA Seq: Differential expression model formula
Popular Question 6 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 7 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 9 months ago, created a question with more than 1,000 views. For Design matrix not of full rank.
Student 9 months ago, asked a question with at least 3 up-votes. For RNASeq: Differential gene expression and qqplot
Popular Question 10 months ago, created a question with more than 1,000 views. For Design matrix not of full rank.
Scholar 10 months ago, created an answer that has been accepted. For A: bowtie2-build cannot use multiple cores
Appreciated 11 months ago, created a post with more than 5 votes. For A: LD-decay in a r2 vs distance(cm) plot
Popular Question 11 months ago, created a question with more than 1,000 views. For Design matrix not of full rank.
Appreciated 12 months ago, created a post with more than 5 votes. 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.
Popular Question 14 months ago, created a question with more than 1,000 views. For Design matrix not of full rank.
Scholar 15 months ago, created an answer that has been accepted. For A: bowtie2-build cannot use multiple cores
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: LD-decay in a r2 vs distance(cm) plot
Popular Question 16 months ago, created a question with more than 1,000 views. For RNA-Seq experiment has low fold change

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