Can I pass a fastq file twice in trimmomatic?
I would like to know if I can pass a fastq file in trimmomatic, and then pass again its results.
Also, how can I be sure that a fastq file that I downloaded from public sources has already been trimmed for quality?
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If it is Illumina data and the reads are not the same lengths then it has been trimmed.
You can pass files as many times as you want, now what happens is not always obvious, normally one would expect that nothing will change second times around, but in reality, algorithms may work in unexpected ways, have various initial conditions, thus the second time you might still get changes (I don’t how Trimmomatic works here, I am just pointing out that it could happen even if seems counterintuitive)
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