Entering edit mode
8.7 years ago
tonja.r
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600
As far as I understood the FPKM values from different isoforms are summed together to represent a single FPKM value for a gene. However, cufflinks produces two tracks for one gene:
I run cufflinks twice: with --compatible-hits-norm and without. Reference annotation contained exons and transcripts.
isoforms.fpkm
ENSMUST00000021056.7 - - ENSMUSG00000001027.7 Scn4a - chr11:106179905-106210703 6598 0.0314068 0.00365992 0 0.0109798 OK
ENSMUST00000174877.1 - - ENSMUSG00000001027.7 Scn4a - chr11:106210768-106214602 443 0 0 0 0 OK
genes.fpkm
ENSMUSG00000001027.7 - - ENSMUSG00000001027.7 Scn4a - chr11:106179905-106210703 - - 0.00365992 0 0.0109798 OK
ENSMUSG00000001027.7 - - ENSMUSG00000001027.7 Scn4a - chr11:106210768-106214602 - - 0 0 0 OK
I also run cuffdiff with the same reference annotation and it produced only one track per gene:
ENSMUSG00000001027.7 - - ENSMUSG00000001027.7 Scn4a - chr11:106179905-106210703 - - 0.00444207 0 0.0137161 OK 0.00839146 0 0.0227746 OK 0 0 0 OK 0.00973267 0 0.0263986 OK
Why do cuffdiff and cufflinks produce different results for the same annotation?
