ERROR: "Fragment file is not indexed"

Question

[bioinformatics.girl]

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?

Answer 1

[Mensur Dlakic]

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.

https://github.com/timoast/signac/issues/7

[bioinformatics.girl]

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.

[Mensur Dlakic]

So both files ../fragments.tsv.gz.tbi and ../fragments.tsv.gz do exist and you are allowed to read them?

[bioinformatics.girl]

Yes, correct.