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Old 04-19-2018, 01:52 PM   #1
yueli
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Default trim adaptor Illumina

Hello,

Human RNA-seq dataset was generated from Illumina HiSeq 3000 with 2X100 cycles run.

Do I have to trim the adaptor?

Thanks in advance for great help!

Sincerely,

Yue
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Old 04-19-2018, 05:00 PM   #2
GenoMax
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You can't eyeball millions of reads. Use a program like bbduk (guide) and scan your files. If your data has no adapter contamination you will recover it as is otherwise you will have removed all extraneous sequence from your data.
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Old 04-20-2018, 04:27 AM   #3
yueli
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Thanks for GenoMax!
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Old 04-20-2018, 06:10 AM   #4
yueli
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Thanks for GenoMax's response!

Actually I really do not know the adaptor of my file. My fastq file is human RNA-seq dataset generated from Illumina HiSeq 3000 with 2X100 cycles run.

What can I do at the present stage.

Thanks in advance for great help!

Sincerely,

Yue Li
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Old 04-20-2018, 07:27 AM   #5
GenoMax
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BBMap includes sequences of commonly used adapter sequences (Illumina kits) in a file in BBMap software. Look for that file (adapters.fa) in "resources" directory of software distribution. You can use that file to scan and then trim your data (ref=adapters.fa option for bbduk.sh).
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Old 04-20-2018, 12:17 PM   #6
yueli
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Thanks for GenoMax!
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