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Hi, I have some unpaired scRNA-seq and scATAC-seq data, they are sequencing the same samples, but in separate scRNA-seq and scATAC-seq assays, so the cell barcodes are different in these datasets. How…
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This paper looks really nice: https://doi.org/10.1093/nar/gkad1225
Has ChIP-seq, ATAC-seq, RNA-seq, enough replicates, two groups (for differential binding).
SRA: https://www.ncbi.nlm.nih.gov/b…
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Cell by bin
Visualize in higlass
Cell by peaks (in BED + snap files)
Annotated peaks (genomic intervals) per cell
Genome-wide (not necessarily tied to a gene)
Our Pipelines:
- [ ] We need to cre…
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## Hierarchy of RE
```
LTR (Family) —> L1 (Sub-Family) —> L1_Rod (Gene) —> L1_Rod_dup1 (Transcript)
LTR (Family) —> L1 (Sub-Family) —> L1_Rod (Gene) —> L1_Rod_dup2 (Transcript)
LTR (Family) —> L1 …
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Since epic2 is optimized for diffuse peaks (correct me if it is not), is it OK to run epic2 for narrow peaks, like regular TF ChIP-seq? I'm trying to find differential peaks for ATAC-seq, as I underst…
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helper script to map features to genomic regions as BED files (code exists)
Add all mentioned helper scripts to the respective recipes and link from the main repository to the recipe so it’s always i…
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# 1. 可能是 ATAC-seq 方法的原始文献 (nature methods, 2023)
https://www.nature.com/articles/nmeth.2688
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-bi…
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Would be nice to add the IDR analysis that is currently carried out by the ENCODE pipelines:
https://github.com/kundajelab/atac-seq-pipeline
https://docs.google.com/document/d/1f0Cm4vRyDQDu0bMehHD7P…
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In [ATAC-seq/auyar/](https://github.com/TheJacksonLaboratory/ATAC-seq/tree/master/auyar), there are a number of bash shell scripts (`*.sh`) that need to be unified with the workflow described by auyar…