Question: Calculating short read coverage at genome wide windows for create.set- MEDIPS
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gravatar for oussama.badad
3 months ago by
oussama.badad0 wrote:

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

createset medip-seq • 107 views
ADD COMMENTlink modified 9 weeks ago by Bioconductor Community ♦♦ 0 • written 3 months ago by oussama.badad0
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