Suppose I supply Newbler my own trimming points, so that a new sff file is created, from the original sff file, now with this new information. Additionally I also supply files with adaptor and possible contaminants sequences through the -vs and -vt command options.
In this case will my trimming points appear under the columns "Orig Trimpoints Orig Trimmed Length", and any alterations Newbler does based on the -vs and -vt files I supplied, under the columns "Trimpoints Used Used Trimmed Length"?
Or do the original trimming points, i.e. the ones the 454 sequencing platform originally set by including under-case characters, still prevail and appear under "Orig Trimpoints Orig Trimmed Length", while the ones I set appear under "Trimpoints Used Used Trimmed Length"?