I have designed a simple RNA-seq aligner, the program takes tow files, first is a reads fastq file and the second is a transcriptome fasta file. the goal of this simple naive aligner is to allow whole exons to be deleted with no penalty
I want to compare the results with output from Tophat (or any other RNA-seq aligner ?) and I know that " TopHat uses a multistep alignment process which starts by aligning reads to transcriptome if genomic annotation is available." RNA-Seq Data Analysis
so my question is, Is it possible - for testing purposes - to align reads to transcriptome only using tophat?