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BosingerLab / BALDR

MIT License
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trimmomatic needs MINLEN parameter #12

Open scharch opened 3 years ago

scharch commented 3 years ago

I'm running into a few cases where trimmomatic produces trimmed reads that are just a few bases long. Those can then map thousands or even tens of thousands times to contigs assembled by Trinity. In turn, that means that the bowtie2 quantification step is unable to complete in a reasonable amount of time since it is using -a. The solution is to add MINLEN:36 (I picked an arbitrary number) to the call to trimmomatic.

amit-upadhyay commented 3 years ago

Thank you for pointing this out. I will include this in the next release.