How does autoted check for quality?
I am currently using autoted as part of a shell script to clip ABI
generated sequences prior to being assembled, but frequently it "fails"
reads that look OK when examined with ted. Is autoted using something
besides clip-seqs to edit the trace files?
Looking at the failed trace files, there are not enough n's to warrent
failure by a sliding window of 5 bases finding 2 or more n's - which is my
(possibly inacurate) understanding of how clip-seqs works.
Are there parameters that can be set in autoted that might allow these
sequences to "pass"?
Any help is appreciated!
Don Hutchison
NCI-FCRDC/LCMS
