Colleagues,

I am having trouble running cufflinks with an annotation file on the public 
Galaxy.  The assembled transcripts gtf file has all the FPKM at 0 although the 
gene expression and transcript expression tab files have values for FPKM.

I have seen the SEQanswers threads about the compatibility of tophat bam files 
relative to chromosomes labeled as 1,2,3… versus Chr1, Chr2, Chr3…   I am using 
the iGenomes bovine UMD3.1 genome and annotation file (chromosomes are  1,2,3) 
from the history.  I altered the gtf file to Chr1, Chr2, Chr3… but it did not 
help.

Another potential discrepency/conflict is that the genome and gtf file have the 
bosTau6 database attribute from when I uploaded them. However I am running them 
from the history (bosTau6 is not an option for tophat).  I do not seem to be 
able to remove the attribute.

Am I missing something else?

Here is the command line
Info: cufflinks v1.0.3
cufflinks -q --no-update-check -I 50000 -F 0.050000 -j 0.050000 -p 8 -G 
/galaxy/main_database/files/003/142/dataset_3142240.dat -N -b ref.fa

Here is the details page
Tool: Cufflinks
Name: Cufflinks on data 69, data 4, and data 5: assembled transcripts
Created: Nov 09, 2011
Filesize: 44.6 Mb
Dbkey: bosTau6
Format: gtf
Tool Version:
Input Parameter  Value
SAM or BAM file of aligned RNA-Seq reads  4: Tophat for Illumina on data 4 and 
data 69: accepted_hits
Max Intron Length  50000
Min Isoform Fraction  0.05
Pre MRNA Fraction  0.05
Perform quartile normalization  Yes
Conditional (reference_annotation)  1
Reference Annotation  5: iGen_UMD3_1_genes.gtf
Conditional (bias_correction)  0
Conditional (seq_source)  1
Using reference file  69: UMD31_iGen_1-29X.fa
Conditional (singlePaired)  0

Cordially,
Chris

___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to