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Question: Error in SpliceR and GTF file issue
0
gravatar for mfahim
2.5 years ago by
mfahim0
Korea, Republic Of
mfahim0 wrote:
I got my RNAseq data from Vendor, who used GFF file in TopHat etc. 

1. Can I use GFF file? in other words will SpliceR support GFF or I need GTF?

2. I am getting the following error.. and have no idea what it means..
Creating spliceRList...
Error in strsplit(unlist(lapply(isoformDataSplit, FUN = function(x) { : 
  non-character argument

 

Help from anyone would be greatly appreciated.

 

Have a nice day

Fahim

ADD COMMENTlink modified 2.3 years ago by deppt0020 • written 2.5 years ago by mfahim0
1
gravatar for qinsheng.cn
2.4 years ago by
qinsheng.cn10
qinsheng.cn10 wrote:

Hi! Man.

I meet this error and solved it. I hope my experience will help you.

You'd better check your "readCufflinks" function, it must use "gtfFile =" and "genome =" parameter.

My error disappeared after setting these parameters.

Good luck!

 

ADD COMMENTlink written 2.4 years ago by qinsheng.cn10
1
gravatar for gdy
2.3 years ago by
gdy10
United States
gdy10 wrote:

Hi qxs718, 

I faced same issue when I did cuffdiff without merged.gtf files. 

Basically you need to aligned your bam files to merged.gtf from cuffmerge (that is reference transcriptome) when you execute cuffdiff. 

Then you provide same merged.gtf file to readCufflink

cuffDB <-readCufflinks(rebuild = T, gtfFile='your merged.gtf', genome='hg19') 

In my case it solved the issue.

ADD COMMENTlink written 2.3 years ago by gdy10

It's quite useful for "rebuild = T" 

ADD REPLYlink written 2.0 years ago by sheepyuanyang0
0
gravatar for qxs718
2.3 years ago by
qxs7180
United States
qxs7180 wrote:

Hi I met same problem. My "readCufflinks" used the gtfFile and genome parameters, while I still have this problem.

Any ideas?

ADD COMMENTlink written 2.3 years ago by qxs7180
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