Option for bowtie-build

[ljxue]

Dear all,
In the manual of bowtie:

bowtie-build
--ntoa Convert Ns in the reference sequence to As
before building the index. By default, Ns
are simply excluded from the index and
'bowtie' will not find alignments that
overlap them.



Does this mean that, by default, the total length of reference was shorten than the original sequence? In this case, does the site in the output file consist with the original sequences?

Thank you.

[Ben Langmead]

Does this mean that, by default, the total length of reference was shorten than the original sequence? In this case, does the site in the output file consist with the original sequences?

The coordinate reported in the bowtie output will still be correct.

Thanks,
Ben

[sclindsay]

Hi Ben,

If the coordinates reported are still correct, I'm assuming this means that if I feed a gff file to bowtie then the coordinates will still match?

Thanks,

Scott