1. Align reads from each sample to the reference genome using tophat
For Illumina/basespace data:
For ABI SOLiD (colorspace) data:
The output file (accepted_hits.bam) is the alignment output which will be used in following steps.
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.
Several output files, consisting of raw and normalized counts for genes, isoforms and transcription start sites are generated. More about the output files at cufflinks manual