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I am using the staden-1.6.0 package (the newer could not be installed) and have the following questions:
I am not sure I understand the difference between "quality clip ends" and "quality clip". The latter includes the parameter "minimum average quality at ends", which is 15 by default; apparently it clips reads in contigs (=assembled from more than one read), and extends holes if occuring. What does 15 refer to? Is this a confidence value coming from phred, i.e. *.qual?
"Quality clip ends" seems to clip ends of contigs (=assembled from more than one read,that is left and right ends of contigs), but what are the cutoffs?
Both quality clip ends and quality clip do not seem to clip singlets. Is that correct? And if so, is there a tool that clips contigs ends and singlets ends?
Any comment is greatly appreciated.