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roblanf / sangeranalyseR

functions to analyse sanger sequencing reads in R
MIT License
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Regarding sangeranalyseR package #79

Closed Ruddhida closed 2 years ago

Ruddhida commented 2 years ago

i am getting an error as "trim.mott not found". what could be the reason for that? and how do i rectify it?

looking forward to hearing from you soon.

thanks and regards Ruddhida

R
Kuanhao-Chao commented 2 years ago

Hi @Ruddhida,

We do not implement trim.mott function in sangeranalyseR. I think the function that you are looking for is updateQualityParam. Here is the link to the documentation: https://sangeranalyser.readthedocs.io/en/latest/content/advance_user_SangerRead_ab1.html#updating-sangerread-quality-trimming-parameters

Best, Kuan-Hao

roblanf commented 2 years ago

Just to expand a bit (an sorry for my slow reply here). trim.mott() is a function that was in the old (unreleased) version of SangerAnalyser.

To trim reads with this algorithm (the algorithm is still there, just not the function) you can change the TrimmingMethod parameter.

The default is TrimmingMethod = "M1", which is the Mott algorithm. The alternative is TrimmingMethod = "M2", which is the trimmomatic algorithm.

More details are here: https://sangeranalyser.readthedocs.io/en/latest/content/advance_user_SangerRead_ab1.html, and elsewhere in the documentation.