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Old 07-17-2012, 12:03 PM   #1
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Location: USA

Join Date: Feb 2012
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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!
wzhang1001 is offline   Reply With Quote
Old 07-17-2012, 01:38 PM   #2
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Location: Halifax, Nova Scotia

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You can use PRINSEQ
As far as I remember you can tell the program to trim a certain amount of bases from either end.
You can also do this with Galaxy:

Prinseq may be better as you will retain your Q data.

If you wanted to sort your amplicons while you remove primers and adapters you could use jMHC
For this you need to know your primer sequence but you should be able to figure out what your primers were from your sequence.
JackieBadger is offline   Reply With Quote
Old 07-18-2012, 06:17 AM   #3
Location: FL

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Posts: 19

You can try

cutadapt :
fastx clipper :

Tha cutadapt has more options.
jlli is offline   Reply With Quote
Old 07-18-2012, 06:23 AM   #4
Location: Sweden

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You can also try

Trimmomatic :
Krish_143 is offline   Reply With Quote
Old 07-19-2012, 11:32 AM   #5
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Join Date: Feb 2012
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Hi all,

Thank youf or all your help!
wzhang1001 is offline   Reply With Quote

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