Hi Johanna,

This may be related to a prior known problem that I see in one of your parameters. Would you please share your history with me so that I can double check and provide feedback? Use the gear icon above the History pane and choose "Share or Publish", then click on the first button on the center form to generate the link, copy and email that back to me directly (not to the mailing list).

Thanks for reporting the problem! Sorry for any confusion it caused,

Jen
Galaxy team

On 10/11/13 12:23 AM, Johanna Sandgren wrote:

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:

stdout

Tool Standard Error:

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)

 



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