Hello,
I'm working on some RNA-seq data using TopHat/Cufflinks tools.
I need to compare a tissue (3 replicates for each of the 4 time points, paired end) with two other tissues (2 samples, single end, only one time point), is it possible to use CuffDiff?!
I try to run it, but the differential splicing between the first tissue and the second (for example, "day0 tissue1" vs "sample1 tissue2" or "day0 tissue1" vs "sample2 tissue2") doesn't work, but I see a different splicing in expression bar plot in some genes.
Thank you very much.
I'm working on some RNA-seq data using TopHat/Cufflinks tools.
I need to compare a tissue (3 replicates for each of the 4 time points, paired end) with two other tissues (2 samples, single end, only one time point), is it possible to use CuffDiff?!
I try to run it, but the differential splicing between the first tissue and the second (for example, "day0 tissue1" vs "sample1 tissue2" or "day0 tissue1" vs "sample2 tissue2") doesn't work, but I see a different splicing in expression bar plot in some genes.
Thank you very much.
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