Can readfish reject reads <200bp?

[chilampoon]

Hi there, I was wondering if readfish can reject reads with <200bp being sequenced? because cDNA molecules are usually ~1kb long... in your paper you said rejected read N50 is ~ 4 or 500+ bp, and is there any way to speed up?

thanks

[mattloose]

This is currently the effective limit - i.e 4-500 bp. We actually map the reads within about 150-200 bases, but the turnaround time for the complete analysis results in the final read being around 4-500 bases.