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Old 12-18-2014, 04:36 AM   #1
nouse
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Default Removal of adapters and barcodes

Hi!

I want to compare an existing result from QIIME to cd-hit-otu-illumina.


cd-hit asks

"Barcodes should be removed. All the tags must start at 5' with the same rRNA primer shared by all rRNA genes (rare wrong base calls or small variations are ok - we will filter and trim them away). "

I know trimmomatic, but i think it can only remove adapters?

Any idea for removal of barcodes and adaptor sequences?

Thank you!
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Old 12-18-2014, 04:49 AM   #2
Zaag
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Trimmomatic can remove anything you put in a fasta file.
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Old 12-18-2014, 09:04 AM   #3
nouse
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oh, i just saw the description of trimmomatic.
Could you please advice me to remove adapters + 8mer barcodes from the unpaired r1 r2 fastq files? I would be very happy!
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Old 12-18-2014, 02:54 PM   #4
Brian Bushnell
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As long as the bar codes occur after quite a bit of adapter sequence, you can just ignore them. For example, if "a" is adapter sequence and "B" is barcode, and your sequence looks like this:

aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaBBBBBBBBaaaaaaaa

...then you can just ignore the last "BBBBBBBBaaaaaaaa" and feed the initial part into a trimming program. Or you can substitute all barcodes for BBBBBBBB. What do you mean by "unpaired r1 r2 fastq files"? If you have r1 and r2 files, they should be paired, and trimmed together.
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