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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.
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.