I am totally confused about the FPKM given by cuffmerge. This is my pipeline:
I have 6 replicates of the sample and run tophat and cufflink to each of them. Then I run cuffmerge and hope I can get gene abundance of this sample but most FPKM are one and some with extremely low value(e-324): my genes.fpkm_tracking file is like this:
about 70%reads could be mapped to the annotation and the cufflink output of each replicates seems ok, this is the genes.fpkm_tracking file of cufflink:
Anyone knows if cuffmerge can give reasonable FPKM values, and if it cannnot, how to get an 'average' gene expression levels of this replicates.
Thanks in advance for advice
Luyi
I have 6 replicates of the sample and run tophat and cufflink to each of them. Then I run cuffmerge and hope I can get gene abundance of this sample but most FPKM are one and some with extremely low value(e-324): my genes.fpkm_tracking file is like this:
Eif2s2 - - Eif2s2 Eif2s2 TSS1774 2:154697145-154718642 - - 4.94066e-324 4.94066e-324 4.94066e-324 OK
Cbfa2t2 - - Cbfa2t2 Cbfa2t2 TSS8205 2:154262219-154365092 - - 9.88131e-324 9.88131e-324 9.88131e-324 OK
CUFF.22438 - - CUFF.22438 - - 2:154299058-154299334 - - 1 1 1 OK
CUFF.22439 - - CUFF.22439 - - 2:154329343-154329686 - - 1 1 1 OK
CUFF.22440 - - CUFF.22440 - - 2:154352123-154352545 - - 1 1 1 OK
Cbfa2t2 - - Cbfa2t2 Cbfa2t2 TSS8205 2:154262219-154365092 - - 9.88131e-324 9.88131e-324 9.88131e-324 OK
CUFF.22438 - - CUFF.22438 - - 2:154299058-154299334 - - 1 1 1 OK
CUFF.22439 - - CUFF.22439 - - 2:154329343-154329686 - - 1 1 1 OK
CUFF.22440 - - CUFF.22440 - - 2:154352123-154352545 - - 1 1 1 OK
CUFF.29200 - - CUFF.29200 - - 15:53120262-53120485 - - 10.2459 3.76582 16.726 OK
CUFF.29201 - - CUFF.29201 - - 15:53120618-53120878 - - 6.34698 2.3328 10.3612 OK
CUFF.29202 - - CUFF.29202 - - 15:53121871-53122016 - - 96.5221 54.3964 138.648 OK
CUFF.29204 - - CUFF.29204 - - 15:53122505-53122811 - - 7.2459 3.83015 10.6616 OK
CUFF.29201 - - CUFF.29201 - - 15:53120618-53120878 - - 6.34698 2.3328 10.3612 OK
CUFF.29202 - - CUFF.29202 - - 15:53121871-53122016 - - 96.5221 54.3964 138.648 OK
CUFF.29204 - - CUFF.29204 - - 15:53122505-53122811 - - 7.2459 3.83015 10.6616 OK
Thanks in advance for advice
Luyi
Comment