Trimmomatic output unpaired reads question

[Anna Quaglieri]

Hi there, 

I am running trimmomatic in PE mode and as expected I get 2 files from every fast file: R1_paired and R1_unpaired, for example. 

I can see that the R1_paired (or R2_paired) do not contain adapters any longer but the R1_unpaired fastq files do. Why is it that? I thought every read with adapter would be discarded.

Also, how do you normally treat the unpaired output? Is it better to remove it from further analysis or do you normally align it as SE reads? 

Thanks for your support, 

Anna

[Ken Field]

Anna-

I don't know why the adapters are still there -- that seems like a glitch to me.

However, I usually discard the unpaired reads in any case. They should represent a very small fraction of the reads (< 1%) and the alignment programs are typically easier to run if you are only giving them paired files.

Ken

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Ken Field, Ph.D.

Professor of Biology

Program in Cell Biology/Biochemistry

Bucknell University

Room 203A Biology Building