Why can't I quantify the peaks (scATAC)?
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Entering edit mode
8 weeks ago

I generated /outs files following Cellranger 10X and for the fragment file did:

>  create fragment objects
frags.104 <- CreateFragmentObject(
  path = "fragments_101.tsv.gz",
  cells = rownames(md.101))


> pbmc101.counts <- FeatureMatrix(
  fragments = frags.101,
   features = combined.peaks,
cells = rownames(md.101)

**Error in h(simpleError(msg, call)) : 
error in evaluating the argument 'y' in selecting a method for function 'intersect': [internal] bgzf_seek() failed**

What am I doing wrong here?? I've been trying for days and sincerely do not want to re-generate a new set of files from Cellranger due to time.

Thanks.

Signac ATAC snATAC scATAC • 270 views
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Entering edit mode

You define the object frag.104 with a 4; but you reference object frag.101 with a 1; is this intended?

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Entering edit mode

Yes. It was just mistyped but the error is "Error in h(simpleError(msg, call)) : error in evaluating the argument 'y' in selecting a method for function 'intersect': [internal] bgzf_seek() failed"

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