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Hello,
Could you please let me know where I can get the input files: 904_3_V3.guide_barcode_reads.txt or K562 guide RNA cell identifies (https://www.sciencedirect.com/science/article/pii/S00928674…
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I am noticing that I am losing over 50% of my reads because they are tagged with cell-barcodes that aren't "core" or aren't 1 edit distance away from a "core" cell-barcode. Some of the non-core cell-b…
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Hi, first, thank you for interesting tool to use in single cell
I have a question about SNV output(chr*.putativeSNVs.csv).
When I put input bam file, bam file have 8923 unique cell barcodes,
bu…
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### Description of feature
Hi, I couldn't run the pipeline on some smart-seq datasets which contains only single-end fastq files. I tried with two different samplesheets and get an error that fastq_2…
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Dear Developers,
Thank you for your work. I tried TedSim and manage to simulate a dataset as explained in the vignette.
## Context
The default implementation of TedSim allows for simulation o…
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Hi @haowenz,
I tend to not force use of the 10X barcode include-list since it is possible there could be valuable information/real cells, but I noticed that some scATACseq data processed via `chromap…
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Hi,
The function `find_nonambient_barcodes` lists the input requirement:
`orig_cell_bcs (iterable of str): Strings of initially-called cell barcodes.`
However, because the default meaning of …
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Currently, if one wants to count reads with differential hashes, in genes, one needs to grep/search the ENTIRE 22-gigabyte channel bam file for one single cell (out of ~700,000), which is extremely in…
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CellClones class should have barcodes and cell types. Clones could be constructed afterwards. Some algorithms take barcodes and cell types as inputs, while other might take clones (could be reconstruc…
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Hi,
Thank you for developing a useful tool.
I am confused about the output of sEV_recognizer function. The n_obs of raw_SEVtras.h5ad file has 1129,431 lines, nearly 10 times more cells than my orig…
HZT55 updated
3 months ago