> Hi,
> 
>>However I am not convinced that this will produce an good assembly...
> 
>>I have seen better peaks in my life. ;)
> 
> Yeah, that's why I just quit the job after looking at the distribution.
> 
> I've decided to go with a trimming method that just chops everything off 
> below Q=30.  This will leave me with number of very short reads, but also 
> keep many full 
> length reads that are of very good quality. 

You peak will be more explicit with less sequencing errors so filtering below 
Q=30 is a good idea for your data.

> I'm reluctant those short reads out however, because it would muddle the 
> paired end ordering, and it appears that it would be a fair amount of work 
> and somewhat of a waste to > also throw out the other pair that might be a 
> reasonable enough read.  But, how would Ray deal with reads that might be 
> below the Kmer length?  Would this cause a problem?
> 
> Walter

They will be skipped.

    Sébastien
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