Cummerbund Returns 0 Sample
3
0
Entering edit mode
7.7 years ago

When running readcufflinks on the default folder containing our 3 samples it returns "0 sample". I tried readcufflinks on the sample folders provided by the package and it works well. I set up R default folder under the root as R_data so technically it should find the samples automatically.. What would be a good solution so readCufflinks can find our 3 samples?

   # Test with our set of 3 samples
library(cummeRbund)
cuff

CuffSet instance with:
0 samples
0 genes
0 isoforms
0 TSS
0 CDS
0 promoters
0 splicing
0 relCDS

# Test with the sample files provided with the cummeRbund package, works fine
cuff
CuffSet instance with:
3 samples
400 genes
1203 isoforms
662 TSS
906 CDS
1062 promoters
1986 splicing
990 relCDS

cuffdiff cummerbund • 3.0k views
1
Entering edit mode
5.5 years ago
lkw222 ▴ 30

Did either of you find a solution to this problem? I am having the same issue as in the original post.

1
Entering edit mode
4.0 years ago
vincr ▴ 10

I have solved this by:

• using R version 3.1.3 or anterior

Hope that helps...

0
Entering edit mode

hi,

I have the same problem. I tried your rebuild command and it didn't work. But I am terrible at coding anyway so I thought I missed something. I have attempted to feed the command by modifying it and this was what i got. What do you suggest I do? Thanks, Efraim

0
Entering edit mode
5.6 years ago
super ▴ 60

I have similar questions but no one knew the answers.

CuffSet instance with: 2 samples 25264 genes 0 isoforms 0 TSS 0 CDS 0 promoters 0 splicing 0 relCDS

but I have 6 samples (3 samples in 1 group), I don't know why it happened.