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Old 09-09-2014, 08:56 PM   #1
mot
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Location: Taiwan

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Default illumina bcl2fastq remove adaptor

I am running bcl2fastq 2.14. I do not find the parameters about remove adaptors.
The default will remove adaptors. If I do not want to remove adaptors, what can I do?
Thank you for help!!
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Old 09-10-2014, 04:04 AM   #2
GenoMax
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Default

This seems to be the case for bcl2fastq v. 2.15.0.4 also (based on some other posts here, you should upgrade to this version).

We have not worked with NextSeq data as yet but this is a feature that should be present.
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Old 03-30-2016, 04:29 AM   #3
thyh2
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Quote:
Originally Posted by mot View Post
I am running bcl2fastq 2.14. I do not find the parameters about remove adaptors.
The default will remove adaptors. If I do not want to remove adaptors, what can I do?
Thank you for help!!
The bcl2fastq need a sample sheet as input. At the third section called '[Settings]'. You can add your own adapter to it, then bcl2fastq will read the adapter from sample sheet to trim adapter in the reads.

If you don't want to remove adapters, just do not add your adapter sequence to the sample sheet.
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