Entering edit mode
6.0 years ago
bioinforesearchquestions
▴
370
Hi,
With the below cuffdiff output, I already generated plots using cummeRbund package. But now, I am getting some error. What could be the reason? Have anyone faced it before?
cuff_data <- readCufflinks("/Users/admin/Desktop/RNA_seq_Analysis/cuffdiff", rebuild = T)
Creating database /Users/admin/Desktop/RNA_seq_Analysis/cuffdiff/cuffData.db
Reading Run Info File /Users/admin/Desktop/RNA_seq_Analysis/cuffdiff/run.info
Writing runInfo Table
Reading Read Group Info /Users/admin/Desktop/RNA_seq_Analysis/cuffdiff/read_groups.info
Writing replicates Table
Reading Var Model Info /Users/admin/Desktop/RNA_seq_Analysis/cuffdiff/var_model.info
Writing varModel Table
Reading /Users/admin/Desktop/RNA_seq_Analysis/cuffdiff/genes.fpkm_tracking
Checking samples table...
Populating samples table...
Error: Columns `index` not found
In addition: There were 50 or more warnings (use warnings() to see the first 50) >
cuff_data
CuffSet instance with:
0 samples
0 genes
0 isoforms
0 TSS
0 CDS
0 promoters
0 splicing
0 relCDS
Why you are using
rebuild = T
option? Have you tried without using that option?Yeah, tried without that as well. Same error and empty cuffset instance.
Can you please post the output of this command: