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-G transcripts.gtf can be used to align to transcriptome first and align only those that don't map to transcriptome to the genome. This is useful for speeding up tophat
2. Assemble transcripts using cufflinks on each alignment result
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Several output files, consisting of raw and normalized counts for genes, isoforms and transcription start sites are generated. More about the output files at http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff_output
4b. Check for differences between the assembled transcripts and known transcripts.
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