Cuffdiff output question

[jdanderson]

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?

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

[adarob]

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