Hi all
i am trying to create set for my medipseq data , here is my command
AKM-ANF_MeDIP = MEDIPS.createSet(file = "/scratch/obadad/MEDIP-Seq_BAMs/AKM-ANF-mapped.sorted.bam", BSgenome = "BSgenome.Oeuropaea.IOGC.v1", extend = 300, shift = 0, uniq = 1e-3, window_size = 100, paired=T)
everything is good till it gets to Calculating short read coverage at genome wide windows...
All chromosomes in the reference BSgenome will be processed: [1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" "13" "14" "15" [16] "16" "17" "18" "19" "20" "21" "22" "23" Reading bam alignment AKM-ANF-mapped.sorted.bam considering 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 using bam index Total number of imported short reads: 94574662 Extending reads... Creating GRange Object... Keep at most 2 read(s) mapping to the same genomic location Number of remaining reads: 70758499 Calculating genomic coordinates... Creating Granges object for genome wide windows... Calculating short read coverage at genome wide windows... Error in AKM - ANF_MeDIP = MEDIPS.createSet(file = "/scratch/obadad/MEDIP-Seq_BAMs/AKM-ANF-mapped.sorted.bam", : *object 'AKM' not found*
