Re: [Mapass-help] Getting all hits for reads

[Heng Li <lh...@gm...>]

Hello David,

Thanks for the e-mail. Unfortunately, mapass2 only stores the best  
hit and if there are multiple equally best hits, mapass2 will  
randomly choose one. Mapass2 is designed in this way because it only  
uses the best hit in SNP calling. Another important reason is storing  
all the hits is sometimes formidable. For example, if there a 32-mer  
exactly appears 1000 times in the genome, storing one best hit for  
each read requires 1,000-unit memory for 1X. However, if all the best  
hits are stored, 1,000,000-unit memory will be consumed. For the  
large-scale alignment, this price is too high.

Hope this may explain the reason why mapass2 cannot give all the hits.

with kind regards,

Heng



On 2 Jul 2007, at 17:36, David H. Spencer wrote:

> Heng,
>
> I would like to get ALL the best hits for each read, but the 'mapview'
> function and '-N' option only seem to return one best hit. Is there a
> way to get mapass2 to give me all of the matching positions for each
> read that have the best score (eg, all the hits for a read that  
> matches
> an exact repeat in the genome). Thanks!
>
> David Spencer
>
> University of Washington
> Dept. of Genome Sciences
> Seattle, WA