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Default trimming adapter sequences don't match documentation #13

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kubu4 opened this issue Jul 21, 2022 · 0 comments
Open

Default trimming adapter sequences don't match documentation #13

kubu4 opened this issue Jul 21, 2022 · 0 comments

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@kubu4
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kubu4 commented Jul 21, 2022

Adapter trimming documentation shows much longer adapter sequences than what the is shown when running the pipeline.

Adapter Trimming
By default the pipeline will assume that pre-trimmed reads have been given to the --input parameter, and will therefore skip the trimming process unless specified. Trimmimg will be performed with cutadapt which takes into consideration a number of additional parameters:

--trim

Specify to enable trimming. [default: off]

--forward

The forward adapter sequence. [default: AGATCGGAAGAGCACACGTCTGAAC]

--reverse

The reverse adapter sequence. [default: AGATCGGAAGAGCGTCGTGTAGGGA]

Pipeline defaults show as this:

image

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