User: rmf
rmf • 1.0k
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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
rmf • 1.0k
1
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1
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... 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? ...
1
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1
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... 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
rmf • 1.0k
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1
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... If I have multiple annotations (gff/gtf files) for a genome, are there tools/metrics to evaluate which annotation is better? ...
written 5 months ago by
rmf • 1.0k
• updated
5 months ago by
hugo.avila • 180
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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
rmf • 1.0k
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... 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 ...
written 12 months ago by
rmf • 1.0k
• updated
11 months ago by
dchatterjee • 30
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... 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 ...
0
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584
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... 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:
...
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... 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 ...
written 18 months ago by
rmf • 1.0k
0
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0
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3.7k
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... 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
rmf • 1.0k
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17 days ago,
created a post with more than 20 followers.
For Fast LD computation from VCF files using tomahawk
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3 months ago,
created a question with more than 5,000 views.
For RNA Seq: GC Content extra peak
Appreciated
3 months ago,
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For A: bwa mem: Passing a variable to read group
Popular Question
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For Many Differentially expressed genes but few GO terms
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For Raw counts to TPM in R
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For Removing reads from fastq file based on position
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For Removing reads from fastq file based on position
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For Removing reads from fastq file based on position
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For Removing reads from fastq file based on position
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10 months ago,
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For Many Differentially expressed genes but few GO terms
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created a question with more than 1,000 views.
For Fixing batch effect with seurat integrate
Guru
10 months ago,
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Commentator
10 months ago,
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For C: Filtering a vcf file with vcftools, where is my output?
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10 months ago,
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For Raw counts to TPM in R
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11 months ago,
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For Gene length correction for dge
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11 months ago,
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For A: Similarity between two FASTA files
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For Gene length correction for dge
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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,
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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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