We need to trim both a barcode primer as well as some universal primers from FASTQ files so that we can run the files through QIIME. The QIIME tutorial states how to deal with the barcodes, but doesn't state explicitly what will happen with the universal primers (which were used for the original amplifications). Does anyone have experience with this? Will QIIME trim the universal primers as well or will it leave these in, leaving us with a problem further down the road?
If you are using Qiime, its straight forward, check out the link
http://qiime.org/scripts/split_libraries.html
The default settings in qiime removes the forward primer and barcode, but if you want to retain, in case, you can add -k for primer and -B for barcode.
To remove reverse primer, you have to add one more step
see the link
http://qiime.org/scripts/truncate_reverse_primer.html
If you are using Qiime, its straight forward, check out the link
http://qiime.org/scripts/split_libraries.html
The default settings in qiime removes the forward primer and barcode, but if you want to retain, in case, you can add -k for primer and -B for barcode.
To remove reverse primer, you have to add one more step
see the link
http://qiime.org/scripts/truncate_reverse_primer.html
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