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.cufflinks@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 gene locus sample_1 sample_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 -150.518 588.996 3,86E-05 1 no CUFF.462.1 CUFF.462 - gi|190572091|ref|NC_010943.1|:1680283-1681214 q1 q2 NOTEST 696.628 322.149 -111.266 538.062 7,42E-03 1 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-01 1 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-01 1 no CUFF.632.1 CUFF.632 - gi|190572091|ref|NC_010943.1|:2346561-2347408 q1 q2 NOTEST 351.508 167.567 -106.882 415.844 3,20E-01 1 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-01 1 no CUFF.616.1 CUFF.616 - gi|190572091|ref|NC_010943.1|:2301552-2303180 q1 q2 NOTEST 169.682 744.885 -118.774 462.107 3,82E-01 1 no CUFF.617.1 CUFF.617 - gi|190572091|ref|NC_010943.1|:2295763-2297758 q1 q2 NOTEST 225.933 112.178 -101.011 454.517 5,49E-01 1 no CUFF.9.1 CUFF.9 - gi|190572091|ref|NC_010943.1|:41597-42402 q1 q2 OK 1729.08 2797.07 0.693913 -4.461 8,16E-01 0.000179474 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-01 1 no CUFF.549.1 CUFF.549 - gi|190572091|ref|NC_010943.1|:2043111-2043664 q1 q2 OK 7148.23 11816.4 0.725138 -421.443 2,50E+00 0.000275446 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+00 1 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+00 1 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+00 1 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+00 1 no CUFF.597.1 CUFF.597 - gi|190572091|ref|NC_010943.1|:2250029-2250918 q1 q2 NOTEST 229.389 105.246 -112.403 386.937 0.000109116 1 no

Ateequr Rehman House No. 2 ground floor Blauenstr. 10 79115 Freiburg im Breisgau

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