TopHat 2 with BowTie 1 index? Big no no?

[DonDolowy]

Hi everyone,

without knowing, I have been using Top Hat 2 with BowTie 1 index instead of BowTie 2 index. I have already aligned more than 20 samples before realizing this. Re-doing it would mean more than two weeks of extra work, so my question is if this is highly biased or if I will be missing something?
In that case, I will of course re-do it.

Thanks a lot!

Best regards,

Kevin