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Hi @bnprks ,
Thank you very much for your contribution to multi omics sequencing data, I would like to ask you a question on how to quickly obtain the three omics data matrices you measured. I would…
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Hi,
Thanks for the great tool. Recently I've installed CellBender in an Ubuntu server, and I've been having a problem in which the ckpt checkpoint is not saved, and thus the tool is uncapable of co…
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## Bug Report
### Affected tool(s)
IlluminaBasecallsToSam (possibly ExtractIlluminaBarcodes)
### Affected version(s)
Version:2.26.3
### Description
I am using ExtractIlluminaBarcodes and …
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Hello,
Recently a bunch of variably niche uses have appeared where going more granular than barcode level is desirable - pulling apart the donor composition of the read space/count matrix would be …
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Hi,
I ran scTE with the following options, and it threw an IndexError. I am pasting the details below. Could you please help?
Python version is 3.9. mm39 index was successfully created with scTE_b…
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We want to address two issues here
1. define a new folder structure for profiling experiments
1. identify which of the components will be version controlled.
_I will update this comment periodica…
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Hello,
This is more of a question than an issue, but I would like to run velocyto on bulk, 100x100 RNA-seq. I have 6 samples currently, all with >30m reads. Is there any particular way you would su…
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Hi Mervin,
I have succeeded in getting the output files from scUTRquant but I have no idea if the files are in good shape. For example, when I read the **_heart_10k_v3_fastq.genes.Rds_** in R, the ge…
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Hi,
I am running over the tutorial of 'RNA velocity with kallisto | bus and velocyto.R'.... and I have two lines that I can't run:
`bustools capture -o cDNA_capture/ -c ./cDNA_tx_to_capture.txt -e…
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Hello,
I think the BgeeCall approach to using intergenic regions to select a reasonable threshold to call a gene "expressed" is an excellent idea, and I'm keen to try it out. However it's not clear…