Question about cisTarget_databases

[YMSWhuang]

Hello,

Thanks for this very useful tool for scRNA-Seq analysis. I have a question about cisTarget_databases. When I run these scripts, I found a question

org="mgi"

RcisTarget databases location

dbDir="/mnt/workspace_lgu/hhuang/annotation_document/SCENIC/cisTarget_databases/" myDatasetTitle="SCENIC_VSMC_2" # choose a name for your analysis data(defaultDbNames) dbs <- defaultDbNames[["mgi"]] scenicOptions <- initializeScenic(org=org, dbDir=dbDir, dbs=dbs, datasetTitle=myDatasetTitle, nCores=16) Error in initializeScenic(org = org, dbDir = dbDir, dbs = dbs, datasetTitle = myDatasetTitle, : The following RcisTarget databases were not found:

• /mnt/workspace_lgu/hhuang/annotation_document/SCENIC/cisTarget_databases//mm9-500bp-upstream-7species.mc9nr.feather
• /mnt/workspace_lgu/hhuang/annotation_document/SCENIC/cisTarget_databases//mm9-tss-centered-10kb-7species.mc9nr.feather

I downloaded the the databases from cisTarget databases, I found the newest datasets are mm10refseq-r8010kb_up_and_down_tss.mc9nr.feather and mm10refseq-r80500bp_up_and_100bp_down_tss.mc9nr.feather;

So can I use these new datasets for my analysis or I have to download the mm9-500bp-upstream-7species.mc9nr.feather and mm9-tss-centered-10kb-7species.mc9nr.feather like these error told me, thanks.

Best regards Hongbiao

[zhang-TD]

The same question, thanks for any help!

[probirc]

Hi , Similar question. I can run SCENIC in R (version 3.6.1) with the mm9 feather files and it works beautifully on my data. Had a request to re-run the analysis with mm10 feather files. I simply cannot get 'initializeScenic" to recognize the mm10 feather files. Kind regards

[ronkesm]

I am having the exact same issue. Moving to the pySCENIC implementation for the time being until this is resolved.