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2. Identify differentially expressed transcripts using cuffdiff
If you have more than one replicate for a sample, supply the SAM files for the sample as a single comma-separated list.
| Code Block |
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nohup cuffdiff -o <outputdirectory> <gfffile> <sample1_accepted_hits.bam> <sample2_accepted_hits.bam> <sample3_accepted_hits.bam> &cuffdiff.log & |
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