ge_SF, thanks for the guide, i've been working up from zero R familiarity, so it's taken me a bit of reading to get to this point...
the farthest i've gotten is trying to align my reads to my gff file:
my_bamfile_.io <- interval_overlap(my_bamfile, my_gff)
the error i get when i try this is:
Error in newAGIoverlap(from, to) :
NA(s) present in the strand of 'to' or 'from'.
Is this what you were referring to when you said you ran into problems because your gff file had formatting differences from what the program was expecting?
I'm a bit confused by the sample they provide in the girafe package (from the prepareAnnotation.R file) from miRBase (mouse microRNA sequences "mmu_miR13.gff") because it appears that it's a GFF2 version and they're using it with readGff3. I know that the gff I'm using is GFF3, but I'm not sure how to make my Genome_intervals_stranded object readable by interval_overlap.
Any hints/help you could offer on this?
the farthest i've gotten is trying to align my reads to my gff file:
my_bamfile_.io <- interval_overlap(my_bamfile, my_gff)
the error i get when i try this is:
Error in newAGIoverlap(from, to) :
NA(s) present in the strand of 'to' or 'from'.
Is this what you were referring to when you said you ran into problems because your gff file had formatting differences from what the program was expecting?
I'm a bit confused by the sample they provide in the girafe package (from the prepareAnnotation.R file) from miRBase (mouse microRNA sequences "mmu_miR13.gff") because it appears that it's a GFF2 version and they're using it with readGff3. I know that the gff I'm using is GFF3, but I'm not sure how to make my Genome_intervals_stranded object readable by interval_overlap.
Any hints/help you could offer on this?
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