User: rmf

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rmf1.0k
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Posts by rmf

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Comment: C: 10x to cloupe
... Hmm.. Someone needs to reverse engineer the .cloupe format :) https://github.com/10XGenomics/cellranger/blob/master/mro/stages/cloupe/cloupe_preprocess/__init__.py ...
written 26 days ago by rmf1.0k
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10x to cloupe
... I have my data as "10x" format. barcodes.tsv genes.tsv matrix.mtx How can I convert this to .cloupe format to view in the 10x loupe browser? ...
10x single-cell transcriptomics written 26 days ago by rmf1.0k • updated 26 days ago by swbarnes29.4k
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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 5 months ago by rmf1.0k
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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 5 months ago by rmf1.0k • updated 5 months ago by hugo.avila180
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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 12 months ago by rmf1.0k
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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 12 months ago by rmf1.0k • updated 11 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 12 months ago by rmf1.0k • updated 12 months ago by khorms210
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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 17 months ago by rmf1.0k • updated 16 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 18 months ago by rmf1.0k
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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 18 months ago by rmf1.0k

Latest awards to rmf

Prophet 17 days ago, created a post with more than 20 followers. For Fast LD computation from VCF files using tomahawk
Popular Question 17 days ago, created a question with more than 1,000 views. For PacBio merge runs
Popular Question 3 months ago, created a question with more than 1,000 views. For PacBio merge runs
Great Question 3 months ago, created a question with more than 5,000 views. For RNA Seq: GC Content extra peak
Appreciated 3 months ago, created a post with more than 5 votes. For A: bwa mem: Passing a variable to read group
Popular Question 3 months ago, created a question with more than 1,000 views. For Many Differentially expressed genes but few GO terms
Great Question 3 months ago, created a question with more than 5,000 views. For Raw counts to TPM in R
Popular Question 4 months ago, created a question with more than 1,000 views. For Removing reads from fastq file based on position
Popular Question 5 months ago, created a question with more than 1,000 views. For Removing reads from fastq file based on position
Popular Question 5 months 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 Removing reads from fastq file based on position
Popular Question 10 months ago, created a question with more than 1,000 views. For Many Differentially expressed genes but few GO terms
Popular Question 10 months ago, created a question with more than 1,000 views. For Fixing batch effect with seurat integrate
Guru 10 months ago, received more than 100 upvotes.
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: Filtering a vcf file with vcftools, where is my output?
Epic Question 10 months ago, created a question with more than 10,000 views. For Raw counts to TPM in R
Popular Question 11 months ago, created a question with more than 1,000 views. For Gene length correction for dge
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Similarity between two FASTA files
Good Answer 11 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 12 months ago, created a question with more than 1,000 views. For Gene length correction for dge
Great Question 16 months ago, created a question with more than 5,000 views. For bwa mem: Passing a variable to read group
Popular Question 16 months ago, created a question with more than 1,000 views. For Gene length correction for dge
Great Question 16 months ago, created a question with more than 5,000 views. For Raw counts to TPM in R
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Similarity between two FASTA files
Popular Question 17 months ago, created a question with more than 1,000 views. For Gene length correction for dge

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