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I am working with RNA-Seq from two different samples from the same organism.
Regarding this, I did the alignment with bowtie and I run cufflinks, cuffcompare and cuffdiff.
Now I have the cuffdiff results but I have some doubts about it:
1) q1 q2 OK 3213.22 20244.1 1.84059 -96.9252 0 yes
In this case I do not understand why the p-value was not calculated. Despite this, the difference in the expression level is significant as we expected.
2) NOTEST 630.26 312.267 -0.702273 10.148 0 no
OK 137.478 121.844 -0.120717 0.970212 0.331941 no
Here I do not understand why the firstone has NOTEST result while the secondone is OK. I mean, the lastone has less reads and a smaller difference.
May be this is kind of a newbie-question about cuffdiff results, but I really apreciatte any help.
Regards
Álvaro Pena
Regarding this, I did the alignment with bowtie and I run cufflinks, cuffcompare and cuffdiff.
Now I have the cuffdiff results but I have some doubts about it:
1) q1 q2 OK 3213.22 20244.1 1.84059 -96.9252 0 yes
In this case I do not understand why the p-value was not calculated. Despite this, the difference in the expression level is significant as we expected.
2) NOTEST 630.26 312.267 -0.702273 10.148 0 no
OK 137.478 121.844 -0.120717 0.970212 0.331941 no
Here I do not understand why the firstone has NOTEST result while the secondone is OK. I mean, the lastone has less reads and a smaller difference.
May be this is kind of a newbie-question about cuffdiff results, but I really apreciatte any help.
Regards
Álvaro Pena