Tool For Counting Adapter Dimer: I need metrics NOT trimming
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7.0 years ago
jnowacki ▴ 110

Any tools out there that give adapter dimer metrics? I don't care if they trim or don't trim I just need adapter dimer counts to see how messy our wetlab protocol is.

trimming dna adapter dimer adapters primer dimer • 2.8k views
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7.0 years ago
GenoMax 144k

If you are strictly looking for full adapter dimers you could use that sequence in literal=adapter_seq with bbduk.sh. You can run the program (found in BBMap suite) and it will produce statistics of how many reads would be trimmed (except if you don't provide an out= file name, no output files will actually be produced). Look at various reporting options to get additional stats. Use minlength=/maxlength= combination to count only those reads that are dimers.

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7.0 years ago
chen ★ 2.5k

Try AfterQC (https://github.com/OpenGene/AfterQC), its report will give how many reads having adapters, and how many bases are adapter bases. It requires pair-end sequencing.

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but does it report dimers? I'm not concerned with adapters. I'm concerned with adapter dimers that have not library sequence.

Thank you for the response.

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