Alignments error while using `PairedGuideSet` object as input

[abearab]

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:

[Jfortin1]

Hi @abearab,

Yes, addSpacerAlignmentsIterative should work on PairedGuideSet objects, but it seems the data are too big to be handled for the underlying CompressedGRangesList class from the GRanges package; I'll work on a fix, but in the meantime, I'd suggest to do some filtering on your individual gRNAs before pairing them to reduce the size of the object, or alternatively, split your PairedGuideSet object into a list of PairedGuideSet objects and apply the functional sequentially.

[abearab]

Got it, thank you for your response. I'll get back to you if I ran to another related issue.