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roblanf / sangeranalyseR

functions to analyse sanger sequencing reads in R
MIT License
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base calling #71

Open ramiroricardo opened 3 years ago

ramiroricardo commented 3 years ago

Hi @roblanf ,

Thank you for developing sangeranalyseR, we have been testing it for some applications and it is quite interesting.

One doubt we have is what method is being used for the base calling? and could it just take the base calling directly from the raw ab1 file?

best,

Ramiro

Kuanhao-Chao commented 3 years ago

Hi @ramiroricardo,

We use the base calling method in sangerseqR. So basically what it does is to get the maximum peak value for each channel in each peak window.

If you want to use sangeranalyseR to check the base calling result, you can create a SangerRead object and it stores all raw information that's needed for base calling. And if you want to visualize the base calling result, you can simply run the chromatogram() function.

Following are codes that you can try:

inputFilesPath <- system.file("extdata/", package = "sangeranalyseR")
A_chloroticaFFN <- file.path(inputFilesPath,
                             "Allolobophora_chlorotica",
                             "ACHLO",
                             "Achl_ACHLO006-09_1_F.ab1")

 sangerReadF <- new("SangerRead",
                     readFeature  = "Forward Read",
                     readFileName = A_chloroticaFFN)

# chromatogram plot
chromatogram(sangerReadF)

You can also run SangerContig or SangerAlignment functions to do the Sanger seq data analysis and get the base calling result from shiny apps.

For more information, please check the development version of sangeranalyseR documentation.

Please let me know if you have any questions.

beast,

Howard