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

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!

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.

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

Any ideas?