Joakim Westberg jockew at biochem.kth.se
Thu Apr 1 07:02:22 EST 1999


I am looking for a standard procedure for calculating the readlength of sequencing traces. Phred20 seems to be one way of evaluating the reads. Does anyone know how to calculate the readlength of a sequencing trace at Phred20? What does Phred20 exactly mean? One explanation I have got is that all bases are counted that have a quality value of 20 or more with the Phred program. That results in a much shorter readlength than manualy evaluation of the readlength. Could it instead be a stretch of sequence that have an average quality value of 20?
I have tried to run phred with the commando line:
Phred -trim_alt "" -id Test -st xbap -sd Test_out
where Test is my document with chromatograms.
This gives me a basecalling value, but I do not know if it is at Phred20.
Does anyone know of another system for calculating the readlength?

Best wishes,

Jokim Westberg
Dept of Biotechnology
S-10044 Stockholm

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