Error in SpliceR and GTF file issue
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mfahim • 0
@mfahim-7714
Last seen 7.2 years ago
Korea, Republic Of
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

SpliceR Cuffdiff • 1.6k views
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qinsheng.cn ▴ 10
@qinshengcn-8466
Last seen 7.2 years ago

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!

 

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gdy ▴ 10
@gdy-8741
Last seen 7.1 years ago
United States

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.

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It's quite useful for "rebuild = T" 

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qxs718 • 0
@qxs718-8683
Last seen 7.1 years ago
United States

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

Any ideas?

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