How to provide 2 adapter sequences into GB-eaSy_parameters.txt

dpwickland / GB-eaSy

Bioinformatics pipeline to process genotyping-by-sequencing (GBS) data

MIT License

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How to provide 2 adapter sequences into GB-eaSy_parameters.txt #3

Open mictadlo opened 5 years ago

mictadlo commented 5 years ago

Hi, According to GB-eaSy_parameters.txt I can only provide one adapter sequence.

#adapter sequence
ADAPTER_SEQ=GATCGGAAGAGCG

However, we have 2 adapter sequences (forward=CTCGGCATTCCTGCTGAACCGCTCTTCCGATCT and reserve=CWGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAG).

How is possible to provide 2 adapter sequences into GB-eaSy_parameters.txt?

Thank you in advance,

Michal

dpwickland commented 5 years ago

The GBSX software utility (https://github.com/GenomicsCoreLeuven/GBSX) used by GB-eaSy cannot handle more than one adapter sequence. Since your reverse adapter sequence is (essentially) the reverse complement of the forward sequence, you might try just using the forward sequence as the ADAPTER_SEQ parameter; it's possible that GBSX automatically considers the reverse complement of the adapter sequence, although I can't say for sure.

Another suggestion is to run GB-eaSy twice, once with the forward adapter sequence and once with the reverse, and compare the results. There is some debate as to whether adapter trimming is necessary, particularly for reference-based alignment, so the choice of adapter here may not affect your final results.