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Question: Error while running SomaticSignatures
0
gravatar for poojitha.ojamies
2.2 years ago by
poojitha.ojamies0 wrote:

Hi,

I am trying to run soamtic signature on a test data and enountered the following issue. Can someone explain what this problem is and how to fix it? Thanks!

 

> sca_motifs = mutationContext(vr_new, BSgenome.Hsapiens.1000genomes.hs37d5)
Error in .getOneSeqFromBSgenomeMultipleSequences(x, name, start, NA, width,  :
  sequence chr1 not found
In addition: Warning message:
In .Seqinfo.mergexy(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)

ADD COMMENTlink modified 2.2 years ago by Andy Lynch100 • written 2.2 years ago by poojitha.ojamies0
1

What does

seqlevelsStyle(vr_new) 

report? Presumably something different to

seqlevelsStyle(BSgenome.Hsapiens.1000genomes.hs37d5)

?

ADD REPLYlink written 2.2 years ago by Andy Lynch100
2
gravatar for Andy Lynch
2.2 years ago by
Andy Lynch100
United Kingdom
Andy Lynch100 wrote:

I think that 

seqlevelsStyle(vr_new)<-"NCBI" 

should allow you to use your first choice of reference genome.

Best wishes,

Andy

ADD COMMENTlink written 2.2 years ago by Andy Lynch100
0
gravatar for poojitha.ojamies
2.2 years ago by
poojitha.ojamies0 wrote:

Ah, you are right! They are two different builds. Should I use my own FA reference files or is there a better fix for this?

> seqlevelsStyle(vr_new)
[1] "UCSC"
> seqlevelsStyle(BSgenome.Hsapiens.1000genomes.hs37d5)
[1] "NCBI"    "Ensembl"

ADD COMMENTlink written 2.2 years ago by poojitha.ojamies0
0
gravatar for poojitha.ojamies
2.2 years ago by
poojitha.ojamies0 wrote:

Fixed! I used BSgenome.Hsapiens.UCSC.hg19 insead and it works :)

Thanks for the pointer!

 

ADD COMMENTlink written 2.2 years ago by poojitha.ojamies0
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