Re: [maq-help] Text output format

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

On 23 May 2008, at 20:42, Shaun Jackman wrote:

> Two more questions:
>
> "1) Maq maps a repeat read randomly"
>
> Are the multiple alignments stored in the map file, or are the  
> multiple
> alignments already lost by this point?

Multiple hits are not stored in the .map file. If you want to get all  
hits, please use the latest maq version and do alignment with "maq map  
-H"

> If I have a FASTA file without quality information, I can convert it  
> to a FASTQ
> file for use with MAQ by using some constant quality value for every  
> base. Is
> 40 (the letter I in FASTQ, ASCII 73) an appropriate value to use?

I would recommend to use something like 25, which is about the average  
quality of a base.

all the best,

Heng