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I have been using pySCENIC on a few datasets locally but have been looking into larger datasets that required me to move to an HPC infrastructure.
My dataset is not huge, around 10k cells and 17k gen…
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Hi, I have used minimap2 with the following settings:
`minimap2 -ax splice -t 20 --split-prefix tmp_test 4081.ref.fa Tomato_polyA_reads.fastq -o Tomato_polyA.sam -y`
And I have some questions abou…
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Hi,
Comparing the count matrices of cellranger 3.1.0 and star 2.7.3a for 10x v3 single cell data I noticed that star retrieved 3.8% less counts than cellranger.
I restricted the count matrices t…
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Regarding some genes / some regions of genes annotation could be false positive / difficult due to the presence of duplicated region. Would it be possible to annotate this on the gene page or somethin…
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Hi!
I am trying to upload some expression data that I have uploaded before, just for a different analysis. When I run the job, the first and last messages are what I expected (the warning about rol…
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The orgDb reduces genes to almost half ~25K; whereas EnsDb (albeit older release) retains 50K. Add an explanation and look into the differences
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From Andrew Collins:
One feature that I would suggest changing is the inclusion of Orphon genes (e.g. IGHV1/OR15-1*01). This is something I discussed with Gur today at length. VDJbase reports a sur…
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Hi,
When I run LIRICAL I get a "Could not identify gene" error, repeated for every variant. See snippet below:
```
AX747861[ERROR] Vcf2GenotypeMap - Vcf2GenotypeMap.javaorg.monarchinitiative.l…
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Hi I run RADIA in my samples and I got this alleles in the calling:
A
B
C
G
K
M
R
S
T
W
Y
Is it normal? How can I deal with them? During the postporecessing of the vcf I am getting a l…
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Hi all,
I have a general question with regards to the algorithm of zUMIs in mapping reads (might be a STAR issue, hope you can give me a direction)
I am getting the most abundant genes in my sam…