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Hello,
Recently, I'm reading the paper, **Single cell transcriptomics reveals spatial and temporal dynamics
of gene expression in the developing mouse spinal cord**. I have some naive problems.
1.…
hahia updated
4 years ago
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Dear Amulet Developers,
First of all, thank you for developing such a great tool!
I have a simple question about the human_autosomes.txt file, which includes a list of chromosomes 1 to 22. When …
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We've recently released an open-source tool to expand the functionality of Cell Ranger to apply to other technologies. We provide a Docker container on an open-source license (see #2) which can be use…
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I want to report some kind of bug/issue that I recognized during my work in Scirpy and has to do with scirpy.tl.define_clonotype cluster (but likely also with scirpy.tl.define_clonotype, although thi…
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As of Cell Ranger 7.0, the initial expected number of cells is estimated by a fairly simple *OrdMag* algorithm if not specified by the user, as described in the [10X Gene Expression documentation](htt…
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Writing genome FASTA file into reference folder...
...done
Indexing genome FASTA file...
...done
Writing genes GTF file into reference folder...
...done
mkref has failed: error building re…
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Hello Cell Ranger team,
I am currently running cellranger-atac count using a SLURM script on a remote server. However, the pipeline crashes during the ATAC_SETUP_CHUNKS stage with the error gzip.Ba…
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Hi,
Im using scanpy 1.4.2 to analyze my data, using the following command:
`sc.pp.highly_variable_genes(heart_cmc, flavor = 'cell_ranger', n_top_genes = 1000)`
However, instead of getting 10…
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This code creates the range `[10, 15, …, 100]`, which is 19 values. Taking those percentiles together with -inf and +inf creates 20 bins (from 21 bin borders), understood.
https://github.com/theisl…
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Hi, is it possible to run SEVtras part I with all the raw cellranger outputs for multiple samples already in an anndata or does it need to be run by providing the raw cellranger outputs separately?