My understanding to alignment tools are quite limited. Any suggestions are quite welcome. There are quite a lot of articles and questions already on this, but I am not able to find an answer in this context.
I am trying to understand what difference does it make to align the reads by using bowtie and tophat and cufflinks.
My data: Illumina short reads, single end reads . I am not interested in isoforms.
Currently I am using bowtie and aligning with 2/3 mismatches. (I am trimming away the barcodes, adapter sequences, also I am trimming the far end of sequences... At the end I have reads of length either 35 to 40). On an average I have about 78 - 80% of reads aligning to genome.
Do you see any limitations in directly using Bowtie over the other tools.