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dbrg77 / plate_scATAC-seq

A rapid and robust plate-based single cell ATAC-seq (scATAC-seq) method
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Inquiry about generating aggregate single cell ATAC-seq profiles #2

Open sallyseullee-0821 opened 10 months ago

sallyseullee-0821 commented 10 months ago

Hi,

I read your Nature publication (https://doi.org/10.1038/s41467-018-07771-0) and would love to generate aggregate single cell profiles in figure 3A and 4D's bottom panel for my data.

Could you kindly provide guidance on how to replicate this? Your insights would be greatly appreciated!

Thanks, Sally

dbrg77 commented 10 months ago

Hi @sallyseullee-0821

Thanks for your interest. Those browser tracks were simply visualised using the UCSC genome browser. You need the bigwig files which were generated during this Snakemake pipeline.

Essentially, you will get a *_treat_pileup.bdg file that contains the signal of ATAC-seq reads along the genome. It is in bedGraph format, generated during MACS2 peak calling. Then the bdg file is converted to *bw format.

To visualise bw, you just need to follow the instructions here:

https://genome.ucsc.edu/goldenPath/help/customTrack.html

I hope this helps.

Xi