Running a pipeline with the following argument:
chrom_assay <- CreateChromatinAssay(
counts=counts,
sep = c(":", "-"),
genome = 'mm10',
fragments = '.../fragments.tsv.gz.tbi',
min.cells = 10,
min.features = 200)
I keep receiving the error `Fragment file is not indexed. Any suggestions?
There is no such a directory as .../ - maybe you meant ../ for one directory up? Either that is wrong, or you don't have the original fragments file (fragments.tsv.gz) in the same directory.
Right; I was demonstrating that I was providing the path of the fragment file. I have tried .tsv, .tsv.gz, .tbi files, etc. Same error.
So both files ../fragments.tsv.gz.tbi and ../fragments.tsv.gz do exist and you are allowed to read them?
Yes, correct.
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