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Hi,
Thanks for this super nice method and the pipeline. In the minimap2 bam outputs, I don't see any junction reads even though minimap2 is run with the `-x splice` parameter. Sashimi plots are all…
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### Description of feature
Hello, thanks for the great work with this pipeline. I would like to try to use this pipeline to call somatic mutations in single cell rna-seq data. I have my own WGS refer…
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As I mentioned above, I am trying to find out what is going on with some flv_trust4 data totally unsuccesfully.
On top of the lack of efficient guidance from the company, we made numerous trials g…
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Hi Jiekai Lab - thank you for developing such great resouce!
I keep on having an issue to create custom genomes for scRNA analysis. Even when I run the example data with:
scTE_build -te ./Data/TE.…
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hi,
Thanks for your great work.:)
I read that log2(TPM+1) data are needed but not UMI gene-barcode matrix from cellranger pipeline of 10x genomics.can UMI count matrix be input by somehow transf…
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Hi there, thank you for putting out this tool!
I was wondering if it could be possible to run brewerIX on the output of ASEReadCounter? As I am working on many scRNA-seq samples it is more efficien…
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Hi,
I am trying to apply the RaceID/StemID pipeline to my scRNA seq dataset, however, even though I am setting the number of clusters to a specific number with this line sc
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**User story**
As a member of the SSR team, who has received a plate from faculty containing cDNA, I would like to be able to import them into Sequencescape along with all the required data.
**Who…
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## Is your feature request related to a problem? Please describe
TRUST4 claims they can call TCRs not only from VDJ-enriched 10x data, but also regular 10x 5' seq and other scRNA-seq protocols.…
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Dear Professors,
Thanks for coming up with this great tool. However, I'm confused with how to use it by the tutorial. In PDAC deconvolution, the tutorial only uses the train_vae function, however,…