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Question: spliceR error with GTF cummeRbund input
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gravatar for weisbeal
19 months ago by
weisbeal10
weisbeal10 wrote:

Hi,

I am having trouble getting spliceR to read Cufflinks/Cuffdiff output parsed by CummeRbund. I used an annotated genome from NCBI (not available in UCSC or BSGenomes) as a reference for my Cufflinks analysis, and generated a merged.gtf file using Cuffmerge, which I used as input for cummeRbund/spliceR. When I try to generate a spliceRList, the command fails with an error:

> cuffDB <- readCufflinks(dir='./timecourse_22', rebuild=TRUE,gtfFile='../../cuffmerge/merged_asm/merged.gtf', genome='poplar')
..cuffDB output with no error messages...
> mySpliceRList <- prepareCuff(cuffDB)
Reading cuffDB, isoforms...
Reading cuffDB, exons...
Analyzing cufflinks annotation problem...
No instances of a Cufflinks annotation problem found - no changes were made
Creating spliceRList...
Error in strsplit(unlist(lapply(isoformDataSplit, FUN = function(x) { :
  non-character argument

The cummeRbund output appears to be ok:
> cuffDB
CuffSet instance with:
     3 samples
     43563 genes
     107981 isoforms
     62278 TSS
     44694 CDS
     87126 promoters
     124556 splicing
     81208 relCDS

Is this an annotation issue? the spliceR manual only describes downloading annotation information from UCSC. Is there a way to load it from an annotated reference genome (gbk/gff/gtf format etc.)?

Thanks!

ADD COMMENTlink modified 6 months ago by lmanchon0 • written 19 months ago by weisbeal10
1

I figured out what was wrong. By default, spliceR removes any chromosome names that do not match the UCSC format. By supplying the flag "removeNonChanonicalChr=FALSE" to the prepareCuff command, the command completed without error.

ie:

> mySpliceRList<-prepareCuff(cuffDB, removeNonChanonicalChr=FALSE)

The error resulted from the fact that all chromosomes were removed (since they are NCBI and not UCSC format) and the script choked at the lack of valid regions. The flag should probably be changed to "removeNonCanonicalChr" and mentioned in the documentation more clearly.

 

ADD REPLYlink written 19 months ago by weisbeal10

Thanks weisbeal.

I was trying to figure out what is causing prepareCuff to fail, as the example set provided by spliceR worked perfectly.

I too have used the flag you mentioned 

removeNonChanonicalChr=FALSE

which solved the error.

ADD REPLYlink written 18 months ago by Gemy Kaithakottil0
0
gravatar for lmanchon
6 months ago by
lmanchon0
lmanchon0 wrote:

- i have the same error although i used removeNonChanonicalChr=FALSE:

mySpliceRList<-prepareCuff(cuffDB, removeNonChanonicalChr=FALSE)
Reading cuffDB, isoforms...
Reading cuffDB, exons...
Analyzing cufflinks annotation problem...
No instances of a Cufflinks annotation problem found - no changes were made
Creating spliceRList...
Error in strsplit(unlist(lapply(isoformDataSplit, FUN = function(x) { :
  non-character argument

i don't know what's wrong, is there a solution ?

thank you --

 

ADD COMMENTlink written 6 months ago by lmanchon0
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