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roblanf / sangeranalyseR

functions to analyse sanger sequencing reads in R
MIT License
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Alignment only forward reads #78

Closed ryamy closed 2 years ago

ryamy commented 2 years ago

Are there any methods to align only forward sequences? Does sangeranalyseR always require both forward and reverse sequence files?

Kuanhao-Chao commented 2 years ago

Hi @ryamy,

sangeranalyseR does not require both forward and reverse reads. You can align only forward sequences. Just put all reads you want to align in the same directory and follow the naming regulation. It should work!

Here is the link to the documentation: https://sangeranalyser.readthedocs.io/en/latest/content/advance_user_SangerAlignment_ab1.html

Best, Kuan-Hao

pavlohrab commented 1 year ago

Hi @Kuanhao-Chao ,

I still have an issue while trying to analyse forward reads only:

ERROR [2023-04-28 14:35:04] PARAMETER_VALUE_ERROR
'REGEX_SuffixReverse' must be character type.
DEBUG [2023-04-28 14:35:04]    >> For more information, please run 'object'.
DEBUG [2023-04-28 14:35:04]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads

I just didn't input anything to the REGEX_SuffixReverse parameter, so it's NULL, as a default value. The version of sangeranalyzeR is 1.10.0

Is there a workaround of error?

Best, Pavlo

Nicfall commented 1 year ago

Anyone have a solution for the error @pavlorhab presented above? I have that same error