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Hi,
bc.export.X_to_mtx() output the previous mtx generated by cellranger 2:
barcodes.tsv genes.tsv matrix.mtx
The latest cellranger generated distinct outputs now:
barcodes.tsv.gz features.t…
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$ scTE
/public/home/zzs000213/.conda/envs/py3118/bin/scTE:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
__import__('pkg_…
l1y1y updated
1 month ago
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I have very basic questions.
I already generated loom files using velocyto from cellranger filtered matrix and bam files. Now if I am interested in running SoupX, do I need to rerun velocyto afte…
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I would like to ask how Trust4 can directly analyze paired-end .fastq format data from the 10X Genomics platform for single-cell analysis, instead of analyzing BAM format data. Can you provide support…
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See the following issues
- gesistsa/rio#315
- tidyverse/readr#1517
Current dependencies of `readODS` are: `c("cellranger", "readr", "stringi", "tibble", "vctrs", "zip")` See below when `readr` …
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Hi,
I am trying to get the fromcellranger pipeline to work on MacOS Catalina 10.15.7
When I run
conda env create -f scTAR_cellranger.yml
(after modifying the yml file prefix to /home/miniconda3/…
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Hi!
I ran cellranger aggr to generated a pooled bam file from several 10X scRNA-seq data (different time points data).
But velocyto could generate loom file from this pooled bam file with the refer…
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Hi,
I find threads doesn't work under the following case and I must set -j > 30 to run this command:
![image](https://github.com/snakemake/snakemake/assets/29703450/dea04ba4-a5c9-4301-a573-8a1b74278…
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First of all, thank you for your quick response to the last issue.
As you answered, I changed to and installed cellranger version 3.0.2 and confirmed that universc was running well with 10x data.
An…
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Hi @hxj5 , I have a question regarding 10X 5' scRNA-seq data.
For 5' sequencing, the read containing cell barcode and UMI contains part of the transcript https://kb.10xgenomics.com/hc/en-us/article…