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: |
|
|
Tool Standard Error: |
|
|
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)