Question: Tool For Counting Adapter Dimer: I need metrics NOT trimming
0
gravatar for jnowacki
2.9 years ago by
jnowacki70
jnowacki70 wrote:

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.

ADD COMMENTlink modified 2.9 years ago by chen2.0k • written 2.9 years ago by jnowacki70
2
gravatar for genomax
2.9 years ago by
genomax84k
United States
genomax84k wrote:

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.

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by genomax84k
0
gravatar for chen
2.9 years ago by
chen2.0k
OpenGene
chen2.0k wrote:

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.

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by chen2.0k

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.

ADD REPLYlink written 2.8 years ago by jnowacki70
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