Hello Ateeq,
It looks like you are working with a bacterial genome. There has been
some limited discussion on the Galaxy mailing list about using RNA-seq
tools with circular genomes, but the best resources are probably the
tool documentation itself (e.g.
http://cufflinks.cbcb.umd.edu/manual.html#gene_exp_diff
http://cufflinks.cbcb.umd.edu/howitworks.html#hdif), the tool author's
Q/A email tophat.cuffli...@gmail.com, and seqanswers.com.
From a quick check, it seems that the 'not significant' result is due
to the value of Test status being NOTEST.
Definition in documentation link above:
NOTEST (not enough alignments for testing)
Hopefully this helps,
Best,
Jen
Galaxy team
On 3/19/12 11:03 AM, Ateequr Rehman wrote:
Dear galaxy user
After running cuffdiff on my two samples (SAM files from bowtie)
i got a list with p and q values, and löast colum is saying abou
significance
with P value, it seems like the comparison should be significant, but in
Q value is 1, and last coumn is saying not significant
any one have an idea, how to interpret it , should we take any
comparsion with less than 0.05 p value as significant or not
tables in excel looks like it
Nay help is welcome
best
Ateeq
test_id gene_id genelocus sample_1sample_2
status value_1
value_2 log2(fold_change) test_stat p_value q_value
significant
CUFF.428.1 CUFF.428-
gi|190572091|ref|NC_010943.1|:1575813-1577629 q1 q2 NOTEST 171.773
605.136 -150.518588.996 3,86E-051 no
CUFF.462.1 CUFF.462-
gi|190572091|ref|NC_010943.1|:1680283-1681214 q1 q2 NOTEST 696.628
322.149 -111.266538.062 7,42E-031 no
CUFF.635.1 CUFF.635-
gi|190572091|ref|NC_010943.1|:2343969-2346219 q1 q2 NOTEST 396.469
223.951 -0.824027 476.902 1,85E-011 no
CUFF.512.1 CUFF.512-
gi|190572091|ref|NC_010943.1|:1840464-1843486 q1 q2 NOTEST 136.314
70.604 -0.949109 422.322 2,41E-011 no
CUFF.632.1 CUFF.632-
gi|190572091|ref|NC_010943.1|:2346561-2347408 q1 q2 NOTEST 351.508
167.567 -106.882415.844 3,20E-011 no
CUFF.941.1 CUFF.941-
gi|190572091|ref|NC_010943.1|:3664426-3665364 q1 q2 NOTEST 282.247
133.798 -10.769 412.254 3,75E-011 no
CUFF.616.1 CUFF.616-
gi|190572091|ref|NC_010943.1|:2301552-2303180 q1 q2 NOTEST 169.682
744.885 -118.774462.107 3,82E-011 no
CUFF.617.1 CUFF.617-
gi|190572091|ref|NC_010943.1|:2295763-2297758 q1 q2 NOTEST 225.933
112.178 -101.011454.517 5,49E-011 no
CUFF.9.1CUFF.9 - gi|190572091|ref|NC_010943.1|:41597-42402
q1
q2 OK 1729.08 2797.07 0.693913-4.461
8,16E-010.000179474 yes
CUFF.956.1 CUFF.956-
gi|190572091|ref|NC_010943.1|:3665445-3669232 q1 q2 NOTEST 518.525
323.653 -0.679966 444.565 8,76E-011 no
CUFF.549.1 CUFF.549-
gi|190572091|ref|NC_010943.1|:2043111-2043664 q1 q2 OK 7148.23
11816.4 0.725138-421.4432,50E+000.000275446
yes
CUFF.872.1 CUFF.872-
gi|190572091|ref|NC_010943.1|:3489557-3490326 q1 q2 NOTEST 220.274
840.662 -13.897 416.179 3,16E+001 no
CUFF.636.1 CUFF.636-
gi|190572091|ref|NC_010943.1|:2348784-2352394 q1 q2 NOTEST 114.384
601.415 -0.927447 414.807 3,35E+001 no
CUFF.605.1 CUFF.605-
gi|190572091|ref|NC_010943.1|:2271979-2275960 q1 q2 NOTEST 217.007
133.837 -0.697264 409.373 4,24E+001 no
CUFF.568.1 CUFF.568-
gi|190572091|ref|NC_010943.1|:2160538-2164415 q1 q2 NOTEST 74.365
377.013 -0.980011 395.097 7,78E+001 no
CUFF.597.1 CUFF.597-
gi|190572091|ref|NC_010943.1|:2250029-2250918 q1 q2 NOTEST 229.389
105.246 -112.403386.937 0.000109116 1 no
Ateequr Rehman
House No. 2 ground floor
Blauenstr. 10
79115 Freiburg im Breisgau
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