[boyzoe]

Try:

./ssaha

(assuming the file is in the current directory, indicated by the dot in Unix). If you tried this:

ssaha

it would look for an installed copy of ssaha on the system path - but it would not try the current directory. At least, that is how recent versions of Ubuntu are configured.

Really thanks, maubp. The problem solved~!

[robs]

@rob

you mean like 200bp 0% error? where Z100 is 97.29% and default is 97.30%??

The same for 500bp reads where the default is better for 0-2% error rates.

[RNM]

I have got somewhat related question, how do I tweak gsMapper parameters in order to get the reads mapped without introducing gaps. I am looking for SNPs and InDels and the gsMapper output (454AllDiffs.txt) shows gaps rather than mismatches. The mappings to the reference sequence looks fine, but when it comes to detecting variants the mapper is not doing what I expected it to do. Is there some extra step that I am missing for SNP/Indel detection? I have also tried AVA, but as my sequence is not an amplicon (far too big than the standard definition of amplicon in 454 terms), AVA isnt of much help either.

[Estefania]

Hello Everybody

I would like to know if it is better to use 1 or more reference genome at a time, using the reference gs mapper, for 454 reads

Thank You