RnaSeqAnalysis < Cores/BioinformaticsCore < TWikiRNASeq Analysis tophat & cufflinks procedure 1. RNA-seq input files for cufflinks Suppose we are given the RNA-seq output files for two experimental conditions, Alpha and Beta. The format the files come in is FASTQ. The file Alpha will have tens of millions of lines like the following: @SOLEXA2:8:1:1:313#0/1 NGCCTCCCAAGTAGCTGGGATTACAGGTGCACATCACCAC <-- the RNA sequence read +SOLEXA2:8:1:1:313
