Question: problem with methylKit of the annotation
0
gravatar for hua.peng1314
5.0 years ago by
hua.peng1314100
China
hua.peng1314100 wrote:

I am dealing with RRBS data follow the manual(https://code.google.com/p/methylkit/). 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 commends 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

 

methylkit • 1.9k views
ADD COMMENTlink written 5.0 years ago by hua.peng1314100
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1481 users visited in the last hour