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**User story**
As a user of the scRNA Core Cell Extraction pipeline, if I have made multiple sets of child tubes from the LRC PBMC Bank plate, I would like to be able to download the driver file for …
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> cat PUMATAC_tutorial-main/PUMATAC/src/singlecelltoolkit/processes/barcode_correction.nf
nextflow.enable.dsl=2
//binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/singlecelltoolk…
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Hello, I hope you can guide me. Download Fastqs from SRA (SRR9843421), it is sequence data from Microwell-seq.
Use
then I used the Drop-seq protocol you posted. The DGE matrix with the following co…
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Hello! Thank you so much for developing & maintaining a great tool :)
Could you please help me figure out why I had to replace NaN values for "Seurat_cell_type" to "Unknown" ?
Following the pyci…
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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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When I use "CITE-seq-Count-R1./ SRR13724311_S1_L001_R1_001.fastq.gz-R2 SRR13724311_S1_L001_R2_001.fastq.gz-t Cmca9_tag_list_utf8.cfa-cbf 1-cbl 16-umif 17-umil 28 -cells 10000-o OUTFOLDER "is always no…
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Dear Dr. Li, I have encountered some problems while studying TRUST4 script commands recently. I hope to receive your guidance:
About barcoderep-filter. py, the first two lines of the report. out in m…
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Hi,
Thank you for developing this software. I would like to try it, but I encountered some problems.
I ran MATES like this:
```python
import MATES
from MATES import bam_processor
from MATES impo…
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Dear Velocyto-experts,
I am trying to perform RNA velocity analysis of 10x single cell data (cite seq) and during my velocyto executions I noticed warnings that the chromosome IDs in my bam files a…
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I ran MIXCR on single cell data TCR data. After exportClones , I saw some rows with the same cell barcodes (tagValueCELL column) but different cloneId. This means one cell belongs to different clonoty…