1. Align reads from each sample to the reference genome using tophat
For Illumina/basespace data:
nohup tophat -p 4 -r <mate-inner-distance> -G <gfffile> <bowtie_index_prefix> <R1.fastq> <R2.fastq> &>tophat.log &
For ABI SOLiD (colorspace) data:
nohup tophat --bowtie1 -C -p 4 -r <mate-inner-distance> -G <gfffile> <bowtie_colorspace_index_prefix> <R1.fasta> <R2.fasta> <R1.qual> <R2.qual> &>tophat.log &
The output file (accepted_hits.bam) is the alignment output which will be used in following steps.
2. Identify differentially expressed transcripts using cuffdiff
nohup cuffdiff -o <outputdirectory> <gfffile> <sample1_accepted_hits.bam> <sample2_accepted_hits.bam> <sample3_accepted_hits.bam> &cuffdiff.log &