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Enhancement: Add option for users to provide a custom adapter file #40

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natgiot opened this issue Jun 17, 2022 · 1 comment
Open

Enhancement: Add option for users to provide a custom adapter file #40

natgiot opened this issue Jun 17, 2022 · 1 comment
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@hariszaf
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enhancement New feature or request

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natgiot commented Jun 17, 2022

It is very common that NGS data contain adapter sequences other than the ones used during library construction, mainly because sequencing centers may sequence many different libraries at the same time. This cross-contamination, and any other project-specific contamination of reads with short sequences, can be handled easily if the user has the option to provide a custom adapter file in PEMA.
Thank you for considering!
@hariszaf hariszaf added the enhancement New feature or request label Jun 18, 2022
@hariszaf hariszaf self-assigned this Jun 18, 2022
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hariszaf commented Jul 8, 2022 •
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This can be done by enabling the fastaWithAdaptersEtc parameter of Trimmomatic; see page 6.
I will implement this for the next pema version.

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