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)
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
i have been reading for a while but no clue, do i have to create a MEDIPset object to define AKM-ANF before create.set
do i have to have the reference genome in the same directory as the BAM files ?
i am a bit lost here , i ll appreciate your help.
cheers
oussama