TopHat2-Cufflinks-Cuffmerge-Cuffdiff for novel transcript detection and expression comparison pipeline (less than 10 N=1 paired-end fastq files)
Estimates gene and isoform structure including novel transcripts, and detect DEG (differentially expressed genes) of the estimated transcripts.
Map short reads to reference genome by using TopHat2.
Estimate gene/isoform structure by Cufflinks, merge them by Cuffmerge and annotated by Cuffcompare.
Detect DEG by cuffdiff.
Input1-10: paired-end sequence fastq file.
Input11: GTF (given by -g option in command line) is used for reference transcript annotation to guide assembly.
Input12: GTF (given by -M option for cufflinks) is used for masked target annotation like rRNA or tRNA to ignore all alignment within transcripts in this file.
Input13: Always you do not have to set this. This is used for null input.