Here's a line from a CuffDiff output (v 1.2.0) where I had used tophat and the -g (RABT option) and supplied an annotation gtf file.
TCONS_00039273 XLOC_029459 Rpl10 X:160336635-160338842 525L1C2 614L5C2 NOTEST 0 0 0 0 1 1 no
in the gene column Rpl10 is listed and no test was performed.
However when I examine the lines which record significant tests I see an entry
TCONS_00348425 XLOC_081856 - chrX:160336617-160339570 429L2S2 614L5C2 OK 0.641861 11.5201 4.16575 -7.16177 7.96474e-13 2.90794e-09 yes
In this case a region chrX:160336617-160339570 was tested and IS significant.
chrX:160336617-160339570 Significant
X:160336635-160338842 NOTEST
The NOTEST is nested within the transcript range that CuffDiff thinks IS significant.
Anyone care to explain this? If allowed to select its own regions it can find significant expression differences. But cuffdiff fails score any significant differences for any region with a gene column. If I use tophat input with a -G option and force it to use a know set of transcripts, I get no significant differences. This is consistent with the -g behavior in that the named regions do not test significant.
Second part what's the best way to see if all my CuffDiff significant regions actually overlap known genes. Obviously I can use a Graphics viewer for one or two but I have thousands to examine. Is there open source code that will do this?
S
TCONS_00039273 XLOC_029459 Rpl10 X:160336635-160338842 525L1C2 614L5C2 NOTEST 0 0 0 0 1 1 no
in the gene column Rpl10 is listed and no test was performed.
However when I examine the lines which record significant tests I see an entry
TCONS_00348425 XLOC_081856 - chrX:160336617-160339570 429L2S2 614L5C2 OK 0.641861 11.5201 4.16575 -7.16177 7.96474e-13 2.90794e-09 yes
In this case a region chrX:160336617-160339570 was tested and IS significant.
chrX:160336617-160339570 Significant
X:160336635-160338842 NOTEST
The NOTEST is nested within the transcript range that CuffDiff thinks IS significant.
Anyone care to explain this? If allowed to select its own regions it can find significant expression differences. But cuffdiff fails score any significant differences for any region with a gene column. If I use tophat input with a -G option and force it to use a know set of transcripts, I get no significant differences. This is consistent with the -g behavior in that the named regions do not test significant.
Second part what's the best way to see if all my CuffDiff significant regions actually overlap known genes. Obviously I can use a Graphics viewer for one or two but I have thousands to examine. Is there open source code that will do this?
S
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