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Hi all,
The main result file of `velocyto` is a 4-layered loom file. I have read a loom file and found they are: `matrix`, `ambiguous`, `spliced`, and `unspliced`, what is the meaning of each layer…
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I've been using STARsolo for single-cell RNA-seq analysis, and I have a question about how it handles SMART-seq data. I understand that SMART-seq does not employ UMIs or cell barcodes, which are typic…
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Hi, I am running the numbat on scRNAseq data, but I am getting error using run_numbat().
I am sharing the ss of the data:
And this is the command I am using and error I am getting.
```
out = …
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I re-ran the STARSolo cell filtering on my raw matrix and would like to get the same Summary.csv file which is generated after initially running STARSolo. Do you know how I can re-create this file wit…
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I ran into the error while pre-processing the data, please let me know how to proceed?
@kou @ctrapnell @Loyale @cusanovich @mjsteinbaugh
> packageVersion("monocle3")
[1] ‘1.0.0’
cds cds
…
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Hello Linnarsson lab,
Thank you for such a great resource!
I have opened your smaller cluster file in python and have sub-setted some of the clusters I am interested in. I was wondering what the…
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Hi Alex,
I am currently trying to do a splicing analysis of some SmartSeq single cell RNA-Seq data, aligned using StarSolo. During this, I have noticed a difference between the splice junction cou…
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Hi,
Would you expect that the UMIFM listed on the quant_metrics.tsv.gz file and the sum of all count on the actual counts.tsv.gz for a particular cellular barcode be the same? I thought so but I co…
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Hi,
I am using kallistobustools, namely `kb ref` and `kb count` commands to build the count matrix of a scRNA-seq dataset.
I have ran `bustools sort` and `bustools text` on output.filtered.bus…
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Hi,
I ran Numbat with WGS CNV as input; however, it always returns the error message 'seqnames' cannot contain NAs.
I don't have any NAs in count_mat_ATC2, df_allele_ATC2, or the segs_consensus …