I would really appreciate someone's input on some issues I am having with my
cuffdiff output for RNAseq data and how it compares with genes I  have
viewed on IGV (or a similar browser) -

1. when I look at my differentially expressed transcripts file (generated
using ensembl hg19 as a reference with chr added on to obtain results with
ensembl gene names) and search for specific genes that I am interested in I
can not find them in my cuffdiff output file - even though I can visualize
these genes on IGV and they look obviously differentially regulated. Also,
given that the cuffdifff output for differentially expressed transcripts
does list all trascripts, including the ones that have not significantly
changed, wouldn't transcripts for these genes be listed anyway, even if my
visual ballparking on differential regulation is not statistically
significant? I would really like to know why I am missing genes from my
cuffdiff output.

2. do you all get a good correlation between the top differentially
expressed transcripts/genes generated from cuffdiff and how the data looks
when visualized on IGV - ie. do your upregulated transcripts really look
upregulated when visualizing? I found that while some validate visually,
some do not which is confusing....

3. when visualizing on a browser, and if different transcripts for one gene
are regulated differently - ie. some are up in your treated sample but some
are done for the same gene - how can you tell which transcriptID from
cuffdiff corresponds with what you are seeing?

Thank you all for your help!

Kurinji

Graduate Student
Johns Hopkins School of Medicine
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