Thank you so much!
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omicsfury •
Adapter trimming WGS Illumina DNA PCR free kit with BBduk
Dear All,
I'm starting the analysis of WGS data prepared with Illumina DNA PCR free kit. I want to remove adapters using BBduk tool. To do that I want to provide adapter sequence in my fasta file. I am confused how should I text the adapter sequence to my fasta file. The adapter sequence in the sample sheet is separated by "plus" sign:
AdapterRead1 CTGTCTCTTATACACATCT+ATGTGTATAAGAGACA
AdapterRead2 CTGTCTCTTATACACATCT+ATGTGTATAAGAGACA
Should I paste the sequence to the fasta file as it is with "plus" sign, or should I remove the sign?
Please help and explain if possible.
Regards!
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1 answer
You should provide them separately as two sequences in the adapter file.
Illumina says the following for DNA PCR-free tagmentation adapters :
The following sequence includes two adapter sequences joined by a plus sign. When performing adapter trimming, the software independently assesses each adapter for trimming.
CTGTCTCTTATACACATCT+ATGTGTATAAGAGACA
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