TopHat2-Cuffdiff for known gene/isoform expression comparison pipeline (less than 10 N=1 paired-end fastq files)
Detect DEG (differentially expressed genes) at a known gene level and a known isoform level. Map short reads to reference genome by using TopHat2. Detect DEG by cuffdiff.<br/>
|Input format||FASTQ (Illumina)|
|Library layout||For paired-end read only|
|Execution time||About 14hours. (3 samples)|
Input1-10: paired-end sequence fastq file.
Input11: GTF annotation file for known gene/isoform.
Input12: Always you do not have to set this. This is used for null input.