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Old 07-17-2012, 11:03 AM   #1
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Location: USA

Join Date: Feb 2012
Posts: 8
Default Amplicon sequencing remove primer & adapters


I have amplicon sequencing experiment with amplicon length between 45 ~124 bases. The sequencing length is 150, which completely covers the amplicon.

I wanted to remove the primers and adapters in the fastq file, which seems to be a little challenging becase we don't know the sequence of primers (but we do know the adapter sequence).

But we know the sequence of amplicons, so I'm thinking if there is any way that I can retrieve the sequence of amplicons from the the fastQ file, which will automatically get rid of both primer and adapters. Of course I need also retrieve the correspnding Q score for the amplicon sequences.

Is there any tool I can use for this purpose?

Thanks in advance for your help!
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