Quick guide for parameters in tophat-cufflinks in nematode RNA-seq analysis
The summary of tophat-cufflinks protocol is like that:
step1: generate a tophat_out folder with bam files
tophat -G genes.gtf <index> sample1_1.fq sample1_2.fq
tophat -G genes.gtf <index> sample2_1.fq sample2_2.fq
step2: generate new .gtf files (assemble isoform)
cufflinks sample1/accepted_hits.bam
cufflinks sample2/accepted_hits.bam