Hi,
I have this week used the new wrapper version of Cuffdiff that you provide that should now include replicate information in output. But there is no resulting files created. Why? I get all the results in the right panel as usual and they are green (no error message) but the they are all empty.. I use bam-files and cuffmerge files that I have gotten result from before (both in spring and during summer- when you upgraded cuffdiff version). I attach below info for one resulting output.
Kind regards, Johanna Tool: Cuffdiff
Name:
Cuffdiff on data 684, data 384, and others: transcript FPKM tracking
Created:
Oct 09, 2013
Filesize:
0 bytes
Dbkey:
hg19
Format:
tabular
Galaxy Tool Version:
0.0.6
Tool Version:
cuffdiff v2.1.1 (4046M)
Tool Standard Output:
stdouthttps://usegalaxy.org/datasets/bbd44e69cb8906b581bffe7ea9e0cd97/stdout
Tool Standard Error:
stderrhttps://usegalaxy.org/datasets/bbd44e69cb8906b581bffe7ea9e0cd97/stderr
Tool Exit Code:
0
API ID:
bbd44e69cb8906b581bffe7ea9e0cd97
Input Parameter
Value
Note for rerun
Transcripts
684: Cuffmerge on data 559, data 618, and others: merged transcripts
Name
MBs
Add replicate
261: MarkDups_Dupes Marked s101_ok.bam
Add replicate
348: s102_MarkDups_Dupes Marked on 256.bam
Add replicate
412: s103MarkDups_Dupes Marked 357.bam
Add replicate
378: s104MarkDups_Dupes Marked 347.bam
Add replicate
425: s105MarkDups_Dupes Marked.bam
Name
Ctrls
Add replicate
701: MarkDups_Dupes Marked688.bam
Add replicate
671: SRR112675MarkDups_Dupes Marked417.bam
Add replicate
433: SRR112673MarkDups_Dupes Marked 343.bam
Add replicate
427: SRR111937MarkDups_Dupes Marked 376.bam
Add replicate
382: SRR112601MarkDups_Dupes Marked 316.bam
Add replicate
384: SRR111936MarkDups_Dupes Marked 328.bam
Library normalization method
geometric
Dispersion estimation method
pooled
False Discovery Rate
0.05
Min Alignment Count
5
Use multi-read correct
Yes
Perform Bias Correction
Yes
Reference sequence data
cached
Include Read Group Datasets
Yes
Set Additional Parameters? (not recommended for paired-end reads)
No
...................................................................................................................................................... Johanna Sandgren, PhD Department of Oncology-Pathology CCK, Karolinska Institutet SE-171 76 Stockholm, Sweden +46-8-517 721 35 (office), +46-8- 321047(fax), +46-708 388476 (mobile)