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We used tophat-cufflink-cuffmerge-cuffcompare-cuffdiff line to detect gene differential expression among samples. The result of cuffdiff shows that there are many new genes and isoforms found. But we don't know how to fetch these new genes' and transcripts' sequenses during our analysis. Could anyone tell us how to use the information on new genes and transcripts provided by cuffdiff and if possible, to get sequences of assembled transcripts including novel transcripts? Thanks!
We used tophat-cufflink-cuffmerge-cuffcompare-cuffdiff line to detect gene differential expression among samples. The result of cuffdiff shows that there are many new genes and isoforms found. But we don't know how to fetch these new genes' and transcripts' sequenses during our analysis. Could anyone tell us how to use the information on new genes and transcripts provided by cuffdiff and if possible, to get sequences of assembled transcripts including novel transcripts? Thanks!