Kory,

Cufflinks quantifies transcripts in parallel, and the inconsistencies that 
you're seeing are likely the result of these processes finishing in different 
order during different runs. To address this issue, you can use the Galaxy sort 
tool.

Ultimately, this is not a Galaxy issue but an issue with the Cufflinks tool. 
You could drop the Cufflinks authors a note if you feel strongly about this 
inconsistency: tophat.cuffli...@gmail.com

Finally, please use the galaxy-user mailing list for questions about tool 
usage. The galaxy-dev list is for local installation and tool development 
questions.

Best,
J.

On Mar 21, 2012, at 10:51 AM, Johnson, Kory (NIH/NINDS) [C] wrote:

> Hello,
>  
> I performed 6 different runs of Cufflinks using the same Reference Annotation 
> on 6 different samples.  I expected the resulting tabular output to be 
> constant given the same Reference Annotation was used each time.  What I 
> found is that there was an inconsistency.
>  
> Specific example, here is top 5 rows from output for one of the six samples:
>  
> tracking_id          class_code          nearest_ref_id gene_id               
> gene_short_name          tss_id    locus      length   coverage               
>  FPKM    FPKM_conf_lo  FPKM_conf_hi  FPKM_status
> NM_001005484 -              -              NM_001005484 -              -      
>         chr1:69090-70008             -              -              0          
>     0              0                OK
> NR_026820         -              -              NR_026820         -           
>    -              chr1:34610-36081             -              -              
> 0              0              0                OK
> NM_001005221 -              -              NM_001005221 -              -      
>         chr1:367658-368597        -              -              0             
>  0              0                OK
> NR_046018         -              -              NR_046018         -           
>    -              chr1:11873-14408             -              -              
> 0              0              0                OK
>  
> Here are top 5 rows from output for another of the six samples:
>  
> tracking_id          class_code          nearest_ref_id gene_id               
> gene_short_name          tss_id    locus      length   coverage               
>  FPKM    FPKM_conf_lo  FPKM_conf_hi  FPKM_status
> NM_001005484 -              -              NM_001005484 -              -      
>         chr1:69090-70008             -              -              0          
>     0              0                OK
> NR_026820         -              -              NR_026820         -           
>    -              chr1:34610-36081             -              -              
> 0              0              0                OK
> NM_001005221 -              -              NM_001005221 -              -      
>         chr1:367658-368597        -              -              0             
>  0              0                OK
> NR_046018         -              -              NR_046018         -           
>    -              chr1:11873-14408             -              -              
> 0              0              0                OK
> NR_024540         -              -              NR_024540         -           
>    -              chr1:14361-29370             -              -              
> 15114.7 9501.21                20728.1 OK
>  
> Here are top 5 rows from output for yet another of the six samples:
>  
> tracking_id          class_code          nearest_ref_id gene_id               
> gene_short_name          tss_id    locus      length   coverage               
>  FPKM    FPKM_conf_lo  FPKM_conf_hi  FPKM_status
> NR_026820         -              -              NR_026820         -           
>    -              chr1:34610-36081             -              -              
> 0              0              0                OK
> NM_001005484 -              -              NM_001005484 -              -      
>         chr1:69090-70008             -              -              0          
>     0              0                OK
> NM_001005221 -              -              NM_001005221 -              -      
>         chr1:367658-368597        -              -              0             
>  0              0                OK
> NR_046018         -              -              NR_046018         -           
>    -              chr1:11873-14408             -              -              
> 0              0              0                OK
> NR_024540         -              -              NR_024540         -           
>    -              chr1:14361-29370             -              -              
> 28376.8 20008.9                36744.6 OK
>  
> As a user, when selecting the same Reference Annotation to be used.  I would 
> expect the index of results by tracking id to be the same.
>  
> Why is this happening?  Why are they not consistent?
>  
> If  were to concat the above results across samples without correcting the 
> indices, my data would be all mixed up.
>  
> I bring this to your attention as someone may not correct the indices before 
> concat and therefore would be doing downstream analysis incorrect concatted 
> data.
>  
> In turn, I would recommend that the index of results be corrected to be 
> constant for a Reference Annotation when selected.
>  
> Thank you in advance for this consideration.
>  
> Best,
>  
> Kory Johnson
>  
> --------------------------------------------
>  
> Kory R. Johnson, MS, PhD
> Sr. Bioinformatics Scientist
>  
> <image001.jpg>
>  
> www.kellygovernmentsolutions.com
>  
> Providing Contract Services For:
>  
> Bioinformatics Section,
> Information Technology & Bioinformatics Program,
> Division of Intramural Research (DIR),
> National Institute of Neurological Disorders & Stroke (NINDS),
> National Institutes of Health (NIH),
> Bethesda, Maryland
>  
> Mailing Address:
>  
> NINDS/NIH
> Clinical Center (Building 10)
> Office 5S223
> 9000 Rockville Pike
> Bethesda, MD 20892
>  
> Contact Information:
>  
> Phone:    301-402-1956
> Fax:           301-480-3563
> email:       johnso...@ninds.nih.gov
>  
> P Green Message:
>  
> Please consider the environment before printing this e-mail.  Thank you.
>  
> Important Message:
>  
> This electronic message transmission contains information intended for the 
> recipient only.  Such that, the information contained herein may be 
> confidential, privaledged, or proprietary.  If you are not the intended 
> recipient, be aware that any disclosure, copying, distribution, or use of 
> this information is strictly prohibited.  If you have received this 
> electronic information in error, please notify the sender immediately by 
> telephone.  Thank you.
>  
> --------------------------------------------
>  
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> 
>  http://lists.bx.psu.edu/

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

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

Reply via email to