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Hi Fumi,
Thanks for your research and datasets, which are definitely my interest. But when I was trying to running the analysis on the five sn-ATAC-seq datasets, I met problems when creating the Ar…
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Matt Ruffalo has provided us a script (https://gist.github.com/mruffalo/bc35452b10df2410a8bb9e52abdf6271) to grab the various versions of pipelines given the hash of the `ingest-pipeline` git reposito…
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First, thank you for compiling this amazing package. I am however trying to create a multiome RNA+ATAC reference object, based on the 10x data available in the SeuratData package, and am running into …
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Upload code for this part of the project
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Hello,
In cellranger-arc for ATAC-seq, how is the primary alignment chosen out of a group of duplicates? Is it random? Or is it based on base quality like picard or mapping quality like samtools? O…
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Hi Alexander P. Wu,
I have some questions about reproducing results on the ICLR paper. 1), how to choose the iroot for each dataset in the construct_dag function. 2) File model.py Line:20-21 Should …
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Hi IGV Team -- we've recently upgrade to IGV 2.17.x from a commit of 2.16 that enables SSO (#1334). After upgrading we found a significant performance degradation with BigWig files. We load ~50 Big…
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I am trying to use the bias pipeline to generate peak and non peak data in order to train a bias model. It was my impression that if I use [find_bias_hyperparams.py](https://github.com/kundajelab/chr…
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@rootze @Sky970415
> seurat_atac
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### Project short name:
ImmuneLung
### Primary Wrangler:
@ESapenaVentura
### Secondary Wrangler:
TBD
### Associated files
* Google Drive: https://drive.google.com/drive/folders/1PGu6yblSlzVM…