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stuart-lab / signac

R toolkit for the analysis of single-cell chromatin data
https://stuartlab.org/signac/
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Seqinfo object #1765

Closed Guliariel closed 3 months ago

Guliariel commented 3 months ago

Hello,

Since my environment does not let me run commands with big files/ lots of memory I am using interactive mode to perform different analysis. Unfortunately when I am working on this mode (it is like an offline mode) I am not able to run this command: chrom.assay <- CreateChromatinAssay(counts = counts.ls[[experim]], fragments = fragment.ls[[experim]], genome = genome, min.cells = min_cell, min.features = min_feat)

The error msg I receive: Error in download.file(url, destfile, quiet = TRUE) : cannot open URL 'https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/chromInfo.txt.gz'

When I run the script regularly (not on the interactive mode) it works .

I would very much appreciate your help in this regard Thank you very much, Gal

# insert reproducible example here
timoast commented 3 months ago

If you are providing the name of a genome to use in the genome parameter, this requires an internet connection to get the information from UCSC. If you don't have an internet connection, you can either leave the genome parameter as NULL or provide a Seqinfo object with the seqinfo for your genome