I have data from 100bp SE sequencing for 4 conditions with 4 replicates/condition. I have a few questions . I used the tuxedo pipeline with the latest cuffdiff 2 ( with DEseq dispersion methods).
I have a modest 188 genes showing up as differentially expressed.
I also have significant differences in the isoform_exp.diff & tss_group_exp.diff and am not sure how to proceed with the information in these files. How are these files different/related to the splicing.diff file?
Can any of these results be reliably gleaned by using SE data?
Thank you in advance.
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