problem with methylKit of the annotation

Question

[hua.peng1314]

I am dealing with RRBS data follow the manual. I met some problem when doing annotation.The problem showed below.

> read.transcript.features("mm9.refseq.genes.bed",remove.unsual=TRUE,up.flank=1500,down.flank=500,unique.prom=TRUE)
> diffAnn <- annotate.WithGenicParts(myDiff25p, gene.obj)
警告信息：
1: In .Seqinfo.mergexy(x, y) :
  Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': chr1, chr10, chr11, chr12, chr13, chr13_random, chr14, chr15, chr16, chr17, chr17_random, chr18, chr19, chr1_random, chr2, chr3, chr4, chr4_random, chr5, chr5_random, chr6, chr7, chr7_random, chr8, chr8_random, chr9, chr9_random, chrM, chrUn_random, chrX, chrX_random, chrY, chrY_random
  - in 'y': chr20, chr21, chr22
  Make sure to always combine/compare objects based on the same reference
  genome (use suppressWarnings() to suppress this warning).
2: In .Seqinfo.mergexy(x, y) :
  Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': chr1, chr10, chr11, chr12, chr13, chr13_random, chr14, chr15, chr16, chr17, chr17_random, chr18, chr19, chr1_random, chr2, chr3, chr4, chr4_random, chr5, chr5_random, chr6, chr7, chr7_random, chr8, chr8_random, chr9, chr9_random, chrM, chrUn_random, chrX, chrX_random, chrY, chrY_random
  - in 'y': chr20, chr21, chr22
  Make sure to always combine/compare objects based on the same reference
  genome (use suppressWarnings() to suppress this warning).
3: In .Seqinfo.mergexy(x, y) :
  Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': chr1, chr10, chr11, chr12, chr13, chr13_random, chr14, chr15, chr16, chr17, chr17_random, chr18, chr19, chr1_random, chr2, chr3, chr4, chr4_random, chr5, chr5_random, chr6, chr7, chr7_random, chr8, chr8_random, chr9, chr9_random, chrM, chrUn_random, chrX, chrX_random, chrY, chrY_random
  - in 'y': chr20, chr21, chr22
  Make sure to always combine/compare objects based on the same reference
  genome (use suppressWarnings() to suppress this warning).
4: In .Seqinfo.mergexy(x, y) :
  Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': chr20, chr21, chr22
  - in 'y': chr1, chr10, chr11, chr12, chr13, chr13_random, chr14, chr15, chr16, chr17, chr17_random, chr18, chr19, chr1_random, chr2, chr3, chr4, chr4_random, chr5, chr5_random, chr6, chr7, chr7_random, chr8, chr8_random, chr9, chr9_random, chrM, chrUn_random, chrX, chrX_random, chrY, chrY_random
  Make sure to always combine/compare objects based on the same reference
  genome (use suppressWarnings() to suppress this warning).
5: In .Seqinfo.mergexy(x, y) :
  Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': chr20, chr21, chr22
  - in 'y': chr1, chr10, chr11, chr12, chr13, chr13_random, chr14, chr15, chr16, chr17, chr17_random, chr18, chr19, chr1_random, chr2, chr3, chr4, chr4_random, chr5, chr5_random, chr6, chr7, chr7_random, chr8, chr8_random, chr9, chr9_random, chrM, chrUn_random, chrX, chrX_random, chrY, chrY_random
  Make sure to always combine/compare objects based on the same reference
  genome (use suppressWarnings() to suppress this warning).
6: In .Seqinfo.mergexy(x, y) :
  Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': chr20, chr21, chr22
  - in 'y': chr1, chr10, chr11, chr12, chr13, chr13_random, chr14, chr15, chr16, chr17, chr17_random, chr18, chr19, chr1_random, chr2, chr3, chr4, chr4_random, chr5, chr5_random, chr6, chr7, chr7_random, chr8, chr8_random, chr9, chr9_random, chrM, chrUn_random, chrX, chrX_random, chrY, chrY_random
  Make sure to always combine/compare objects based on the same reference
  genome (use suppressWarnings() to suppress this warning).

Error in nearest(ranges(g.bed[seqnames(g.bed) == chrs[i], ]), ranges(subject[seqnames(subject) ==  :

I am not sure what the matter is.

The commands are:

> library(methylKit)
> file.list=list("D14_R1_val_1.fq_bismark_pe.sorted.sam","H28-R_R1_val_1.fq_bismark_pe.sorted.sam")
> objs=read.bismark(location=file.list,sample.id=list("D14","H28-R"),assembly="mm9",nolap=FALSE,mincov=10,minqual=20,phred64=FALSE,treatment=c(0,1))

I also check my files:

less D14_R1_val_1.fq_bismark_pe.sorted.sam |grep 'chr20'
less H28-R_R1_val_1.fq_bismark_pe.sorted.sam |grep 'chr20'
less mm9.refseq.genes.bed |grep 'chr20'

It can't find 'chr20'.

Any help? Thanks