Hello All,
I'm wondering why Tophat doesn't allow to pass the --best --strata options to bowtie. ( --best --strata allow to rank and select the alignments according to their number of mismatches; this seems quite a good feature to me).
From other posts I found that is actually quite easy to edit the tophat script to include these options for bowtie. So I'm wondering if there is any reason why the developers have excluded the --best --strata from tophat? Is there any disadvantage (or negligible gain) in enabling them?
Any comment much appreciated!
All the best
Dario
I'm wondering why Tophat doesn't allow to pass the --best --strata options to bowtie. ( --best --strata allow to rank and select the alignments according to their number of mismatches; this seems quite a good feature to me).
From other posts I found that is actually quite easy to edit the tophat script to include these options for bowtie. So I'm wondering if there is any reason why the developers have excluded the --best --strata from tophat? Is there any disadvantage (or negligible gain) in enabling them?
Any comment much appreciated!
All the best
Dario
