The reads are paired end,90 bp. I have tried using bowtie and tophat.Bowtie gave around 85 % of alignment.While tophat gave around 92 % alignment.Although Tophat calls Bowtie, any ideas why the percent alignment is higher in case of Tophat??
As bacteria do not have splice junctions,does running tophat in anyway affect the alignment.How does running tophat with GTF file affect the alignment?
I prefer using tophat since I would like to do differential analysis using tophat output with cufflinks software.Any ideas would be appreciated.