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  • Cuffdiff GTF file ?

    Hi,

    I'm trying to analyze a samples of a mouse stem cell during different stages of differentiation, for that I first aligned the RNA-Seq reads corresponding to the different samples to an index files using tophat and then I processed the Tophat output tough Cufflinks.

    Now I'm trying to compare different samples using Cuffdiff however I've hit a roadblock.

    Initially I was convinced that I had to use with Cuffdiff a GTF file produced by combining with Cuffmearge or Cuffcompare the transcripts.gtf files produced by Cufflinks for the samples being compared, however I've read a on-line tutorial that recommended using instead the GTF that served as index for the Tophat runs.

    Could somebody with more experience point to correct file to use ?

    Thanks in advanced.

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