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Hello, program developer, thank you very much for your program, it helped us a lot .But I ran into some problems. I downloaded the scCAT data of the released embryos and did the SCCAT-seq process oper…
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In the future, all non multiome scRNA-seq experiments should be patched with this strand specificity. Annika can confirm here.
Reference: https://docs.google.com/document/d/18HWBgcL8nrYF90-JcYRWcw…
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Hello!
Thanks again for sharing data and code! Im working through your script to process scATAC-seq fastq files and Im encountering some errors when I trim the demultiplexed fastq files using trim…
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Hi everyone. Great work for the new paper. I'm trying to replicate the results in your joint ATAC-seq and RNA-seq paper. I saw that for the analysis of A549 ATAC-seq, you mention that the procedure wa…
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Hello Chromap Team,
Thank you very much for actively maintaining the chromap!
I recently used Chromap for mapping scATAC-seq data with a barcode whitelist. I found that the log file is a bit co…
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Hi,
I got this error message when I use scBFA for our dataset:
```
Error in asMethod(object) :
Cholmod error 'problem too large' at file ../Core/cholmod_dense.c, line 105
Calls: scBFA ... ge…
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When run the tutorial "https://greenleaflab.github.io/ArchR_2020/Ex-Analyze-Multiome.html"
The output figures are all correct but when I tried to save them:
```{r}
#Save Plot
plotPDF(p1, p2, p3…
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sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblas-…
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Hi,
I have been using MATES for short read data recently and I wanted to try ATAC data only, however, I am not sure how to process the data.
First, to keep multi mapping information, is it necessary…
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- It nearly spends a whole day to simulate, which is inconvenient.
- I encountered an error like this when I try to simulate a 2000cell*150000peak scATAC. Could you tell me how to fix it?
```
Input…