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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:
The text was updated successfully, but these errors were encountered:
Adapter trimming documentation shows much longer adapter sequences than what the is shown when running the pipeline.
Pipeline defaults show as this:
The text was updated successfully, but these errors were encountered: