Hello all!
I am using methylkit to analyze my methylation data in honey bees.
I have converted a reference genome annotation file (gff3 file) to a bed file, then I run
gene.obj=readTranscriptFeatures(system.file("extdata", "amel_OGSv3.2_sorted.bed",
package = "methylKit"))
The msg was that:
Calculating intron coordinates...
Error in convertBed2Introns(bed) : this is not a valid bed file.
My file is like this:
Group1.1 377 436 . . - amel_OGSv3.1 CDS 2 Parent=GB42164-RA
Group1.1 377 436 . . - amel_OGSv3.1 exon . Parent=GB42164-RA
Group1.1 377 79932 GB42164 0.786254 - amel_OGSv3.1 gene . ID=GB42164
Group1.1 377 79932 GB42164-RA 0.786254 - amel_OGSv3.1 mRNA . ID=GB42164-RA;Parent=GB42164
Group1.1 650 969 . . - amel_OGSv3.1 CDS 0 Parent=GB42164-RA
Should I only keep the first 3 required columns, and test it again?
Appreciate your thoughts.
I am using methylkit to analyze my methylation data in honey bees.
I have converted a reference genome annotation file (gff3 file) to a bed file, then I run
gene.obj=readTranscriptFeatures(system.file("extdata", "amel_OGSv3.2_sorted.bed",
package = "methylKit"))
The msg was that:
Calculating intron coordinates...
Error in convertBed2Introns(bed) : this is not a valid bed file.
My file is like this:
Group1.1 377 436 . . - amel_OGSv3.1 CDS 2 Parent=GB42164-RA
Group1.1 377 436 . . - amel_OGSv3.1 exon . Parent=GB42164-RA
Group1.1 377 79932 GB42164 0.786254 - amel_OGSv3.1 gene . ID=GB42164
Group1.1 377 79932 GB42164-RA 0.786254 - amel_OGSv3.1 mRNA . ID=GB42164-RA;Parent=GB42164
Group1.1 650 969 . . - amel_OGSv3.1 CDS 0 Parent=GB42164-RA
Should I only keep the first 3 required columns, and test it again?
Appreciate your thoughts.
Comment