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gersteinlab / PsychENCODE_SingleCell_Integrative

Integrative Analyses across 388 human brain samples at single-cell resolution
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Scripts for procssing snATAC-seq data #1

Open DylanMannKrzisnik opened 1 month ago

DylanMannKrzisnik commented 1 month ago

Thank you for sharing this resource. Although many of the scripts for processing snRNA-seq data are available, where can we find scripts for snATAC-seq data? Or, what would be the best way to use snATAC-seq data from brainSCOPE and create an ArchRProject?

prashantemani commented 3 weeks ago

Thank you for your queries. We have just updated our database to include all the processed snATAC-seq data in our database here: https://doi.org/10.7303/syn51111084.6

We are still working on getting our snATAC-seq pipeline up on Github. Please check back with us later if the above link does not fully meet your needs.

DylanMannKrzisnik commented 3 weeks ago

That's great, thank you!

I am particularly interested in the MultiomeBrain data. According to the link you've provided, this data can be retrieved with the facet dataGroup = "ATACseq". However, I cannot see the ATACseq option for the dataGroup facet (see screenshot).

Perhaps it is better to select analysisType = "Processed_snATACseq" instead (also visible in the screenshot)?

Is there a terminal command line solution for accessing the data, and filtering the data by facet?

Much appreciated.

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prashantemani commented 3 weeks ago

You are very welcome! And yes, it is best to subset things by the "Processed_snATAC" tag. Additionally (that is, by clicking the following as well), you can look under parentID for the specific data types you are looking for.

DylanMannKrzisnik commented 3 weeks ago

Correction: I had previously not taken a proper screenshot of the dataGroup facet.

image

prashantemani commented 2 weeks ago

Hi, Please let me know if this has not been resolved.

DylanMannKrzisnik commented 2 weeks ago

Thank you for the follow-up.

Indeed, the parentID facet includes the "MultiomeBrain-DLPFC" option which should be helpful. In the end, I will be looking to recreate/load a nuclei x peaks ATAC counts matrix. Once we are granted access to the data via the NRGR application protocol, I will be better able to assess whether the search queries correspond to our needs.