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https://mp.weixin.qq.com/s/J8RbqgJtNlnc7bsLJJUPGA
ixxmu updated
1 month ago
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pbmcs
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Hey Mario,
This is related to issue #45. A user of CAT performed the automated training of CGP and got 0 genes from the prediction step. I got ahold of his data, and found that I was able to get ge…
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Hi,
How can I find the joint cluster result?
I integrated a ATAC data with 2129 cells and a RNA data with 2129 cells, but I can only find leiden_cluster with 4258 cells.
I hope to find the joint cl…
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**seqspec split -o split spec.yaml**
Traceback (most recent call last):
File "/software/miniconda3/bin/seqspec", line 8, in
sys.exit(main())
File "/software/miniconda3/lib/python3.9/sit…
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It would be really useful if there were a samtools utility that would allow one to shift read alignments by strand. _e.g._ shift all reads aligning to (+) strand up 5bps and all reads aligning to (-) …
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Hello,
I'm working with a single cell ATAC dataset in an organism with a very large genome (32 Gbp). Therefore, the number of reads is quite high ~300M and I have a lot of candidate peaks:
```
…
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Line 225, run.py [link](https://github.com/labomics/midas/blob/b23feea0df8e13d1fa4a942c9e9b4feba3f24080/run.py#L225)
`o.dims_h[m] = dim if m != "atac" else o.dims_enc_chr[-1] * 22`
should be
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This follows on a bit from #102 and a conversation with @scottgigante and @aopisco just now. We will need to set up a guideline for how to deal with tasks with multiple data archetypes (like data inte…
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Hi all I was hoping to find help here.
I am doing some ATAC_Seq analysis.
I am trying to compare peak callers Genrich (atac-seq specific) and MACS2 for the same dataset
From what I have read, b…