Hi guys, I have a questions about Bowtie2 right now.
My reference include several sequences in different length (imagine trinity assembly, several 'genes' and their variables). I tried to bowtie2-build all sequences separately then map my reads to it (alignment rate A1, A2, A3, A4) and also tried to bowtie2-build all sequences in one big reference (alignment rate B), the results is different (A1+A2+A3+A4 doesn't equal to B and way smaller than B) . I wonder if anyone have encountered this and maybe can help me explain what was going on?
All mapping is using default setting, and alignment rate is from the alignment summary.
Extra question, how reliable and practical is alignment summary output of Bowtie2?
Thanks you. Emily