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.
Cufflinks does accept any bam file as input, but there is one restriction: there must be XS tags for the spliced alignments.
Well, bowtie doesn't do spliced alignment, and bacteria don't splice their RNA, so I don't think that should be a problem in this case, either technically or biologically. But good point regardless, for anyone working in eukaryotes.