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Alignments error while using `PairedGuideSet` object as input

Open abearab opened this issue 2 years ago • 2 comments

Is it possible to run addSpacerAlignmentsIterative on PairedGuideSet object?! I an error running this code:

pairsGuideSet <- addSpacerAlignmentsIterative(
    pairsGuideSet,
    txObject=txdb,
    aligner_index=bowtie_index,
    bsgenome=bsgenome,
    n_mismatches=2
)
R[write to console]: Error in METHOD(x, i) : 
  Subsetting operation on CompressedGRangesList object 'x' produces a
  result that is too big to be represented as a CompressedList object.
  Please try to coerce 'x' to a SimpleList object first (with 'as(x,
  "SimpleList")').


Error in METHOD(x, i) : 
  Subsetting operation on CompressedGRangesList object 'x' produces a
  result that is too big to be represented as a CompressedList object.
  Please try to coerce 'x' to a SimpleList object first (with 'as(x,
  "SimpleList")').

This is the size of my pairsGuideSet:

PairedGuideSet object with 110196 pairs and 4 metadata columns:

abearab avatar Feb 15 '23 01:02 abearab