BFAST indexing

[phatjoe]

Hi,
I've recently been introduced to BFAST. So please bear with me.

I am trying on reads from Illumina (36bp) but how is the -m and -w option determined?

With the reads of <40bp, my reads should best have the key size of 18. I see variations of -m options with 111111111111111111,11111111111111111101 ,1111101110111010100101011011111 and etc. Can someone please explain to me the difference of it?

Thanks in advance!

[nilshomer]

The appendix states that you should make ten indexes, so you need to have ten "bfast index" commands, one for each mask.