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Old 10-11-2010, 09:00 PM   #1
jdanderson
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Location: Davis, CA

Join Date: Sep 2010
Posts: 45
Default Cuffdiff output question

Hello All,

I was wondering if anyone can tell me why the output files of Cuffdiff (eg gene_exp.diff) have several lines for the exact same chromosomal location?

PHP Code:
XLOC_022423    -    chr1:119542966-119544028    q1    q2    NOTEST    0    0    0    0    1    no
XLOC_022424    
-    chr1:119573838-119869926    q1    q2    NOTEST    5.63697    12.469    0.793897    -2.04636    0.0407209    no
XLOC_022425    
-    chr1:119573838-119869926    q1    q2    NOTEST    0    0    0    0    1    no
XLOC_022426    
-    chr1:119573838-119869926    q1    q2    NOTEST    3.51351    2.67564    -0.272426    0.959018    0.33755    no
XLOC_022427    
-    chr1:119573838-119869926    q1    q2    NOTEST    3.34667    3.52713    0.0525201    -0.220693    0.825331    no
XLOC_022428    
-    chr1:119573838-119869926    q1    q2    NOTEST    2.15116    0.857702    -0.919506    3.9536    7.6985e-05    no
XLOC_022429    
-    chr1:119573838-119869926    q1    q2    NOTEST    0    0    0    0    1    no
XLOC_022430    
-    chr1:119870798-119898805    q1    q2    NOTEST    0    0    0    0    1    no 
Thanks,
Johnathon
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Old 10-14-2010, 08:13 AM   #2
adarob
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Default

This just means that that set of transcripts overlap in the given region.
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