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Hi, Rongxin,
SnapATAC is fast and has good performance. I really like it.
when I used snapATAC on my own data from 10X, I found the barcodes in bam file after 'snaptools align-paired-end ' were…
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Hi,
Thanks for a very useful program.
Unfortunately, I have an issue with incorrect assignments after merging samples:
I'd like to use souporcell to find rare donor cells in tissue from bone …
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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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Hi,
thanks for devoloping this tool!
I'm trying to run citecount with 10xGenomics 5kPBMC public data as a test for the tool. in principle, it should work as i have specified a trim of 10. I also u…
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I am plotting a heatmap from a matrix of 8 rows and 2284 columns. The columns are grouped manually by 8 clusters. My intention is to add a gap between clusters as follows:
```{r}
cell_annot
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### Description of the bug
sample.csv:
```
sample,fastq_1,fastq_2,feature_type
NPC_Astro_Diff_aBeta,NovaSeqX_20240927_LH00181_0041_B22TF5VLT3_bcl-convert_KL_NPC_Astro_Diff_20240916_scRNA_10X_Flex_NP…
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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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Dear Alex:
My name is Chen Weng, I'm a postdoc at Whitehead Institute. Thank you for the amazing tool!
We have some dataset that has very long "Cell barcode", up to 43bp. When I try to…
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Hello.
I have 4 snATAC-seq samples from the DNBSEQ-T7 platform, and for each sample, they are mixed with multiple cell lines. For R1, the read length is 50bp, and for R2, the read length is 70bp.
I …