User: rmf

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rmf970
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Posts by rmf

<prev • 139 results • page 1 of 14 • next >
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Comment: C: Evaluate genome annotation quality
... BUSCO is what I use at the moment and was wondering if there was something better. Something like AED scores. Thanks for BEACON. Never heard of that. ...
written 4 weeks ago by rmf970
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Evaluate genome annotation quality
... If I have multiple annotations (gff/gtf files) for a genome, are there tools/metrics to evaluate which annotation is better? ...
genome annotation written 4 weeks ago by rmf970 • updated 4 weeks ago by hugo.avila110
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Comment: C: RNA velocity plot demystified
... Thanks for that. That might be helpful even though I don't understand python code. And the R notebooks unfortunately don't seem to go into so much detail. Anyhow, my question still stands as to what the LENGTH of the arrows mean. ...
written 7 months ago by rmf970
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RNA velocity plot demystified
... Here is an example of RNA velocity from [Manno .et .al 2018](https://www.nature.com/articles/s41586-018-0414-6). ![enter image description here][1] Colour of cells denote cell type. Layout denotes how cells cluster by some measure of similarity. The direction of the arrows denote the future state ...
velocyto rna-velocity single-cell written 7 months ago by rmf970 • updated 7 months ago by dchatterjee30
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Moving data from Seurat to ScanPy
... I am trying to move data from Seurat to ScanPy. It seems like exporting to loom is one of the ways to do it. In R, I am using an example dataset. library(Seurat) library(loomR) lfile <- as.loom(x=pbmc_small,filename="python/pbmc.loom") lfile$close_all() In python, I read it in ...
single-cell R seurat scanpy python written 7 months ago by rmf970 • updated 7 months ago by khorms130
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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 13 months ago by rmf970 • updated 12 months 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 13 months ago by rmf970
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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 14 months ago by rmf970
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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 14 months ago by rmf970
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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 16 months ago by rmf970

Latest awards to rmf

Popular Question 21 days ago, created a question with more than 1,000 views. For Removing reads from fastq file based on position
Popular Question 27 days ago, created a question with more than 1,000 views. For Removing reads from fastq file based on position
Popular Question 4 weeks ago, created a question with more than 1,000 views. For Removing reads from fastq file based on position
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Removing reads from fastq file based on position
Popular Question 6 months ago, created a question with more than 1,000 views. For Fixing batch effect with seurat integrate
Popular Question 6 months ago, created a question with more than 1,000 views. For Many Differentially expressed genes but few GO terms
Epic Question 6 months ago, created a question with more than 10,000 views. For Raw counts to TPM in R
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Filtering a vcf file with vcftools, where is my output?
Guru 6 months ago, received more than 100 upvotes.
Popular Question 7 months ago, created a question with more than 1,000 views. For Gene length correction for dge
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Similarity between two FASTA files
Good Answer 7 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 Gene length correction for dge
Great Question 12 months ago, created a question with more than 5,000 views. For Raw counts to TPM in R
Popular Question 12 months ago, created a question with more than 1,000 views. For Gene length correction for dge
Great Question 12 months ago, created a question with more than 5,000 views. For bwa mem: Passing a variable to read group
Popular Question 13 months ago, created a question with more than 1,000 views. For Gene length correction for dge
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Similarity between two FASTA files
Student 13 months ago, asked a question with at least 3 up-votes. For RNASeq: Differential gene expression and qqplot
Popular Question 14 months ago, created a question with more than 1,000 views. For Gene length correction for dge
Popular Question 15 months ago, created a question with more than 1,000 views. For gff3validator: gff3 validation error
Popular Question 15 months ago, created a question with more than 1,000 views. For RNA Seq: Differential expression model formula
Popular Question 15 months ago, created a question with more than 1,000 views. For Read count correlation between samples
Popular Question 15 months ago, created a question with more than 1,000 views. For RNA Seq: GC Content extra peak
Popular Question 15 months ago, created a question with more than 1,000 views. For Gene length correction for dge

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