about DEG after cuffdiff

[Hoseong choi]

hi all.

i am working on soybean gene expression analysis with tophat/cuffdiff

After cuffdiff run, I could get results about expression of genes from gene_exp.diff file

In some case, I could not determine the exact expression of gene.

For example,

Glyma03g03100.2:1-1121 Healthy 24hpi OK 37.9054 13.4419 -1.49567 -2.46173 0.04 0.769321 no
Glyma03g03100.2:1181-1853 Healthy 24hpi OK 43.4734 13.3734 -1.70077 -2.93749 0.02925 0.658614 no

Glyma03g03100.2 is one gene. According to results, expression of this gene is divided into 2 fragment.

In this case, how can I analysis gene expression of Glyma03g03100??

[dpryan]

Did this happen with all genes or just this one?

I'm guessing that you supplied cufflinks with an annotation file (probably in GTF format). Can you post the lines relevant to that gene? I'm guessing that cufflinks got confused by the formatting for some reason and computed metrics per-exon, rather than per-gene/transcript.