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Analysis of unfiltered raw data (~35M read average per sample) was completed using the Simple Annotation of Metatranscriptomes by Sequence Analysis 2.0 (SAMSA2) pipeline [21] as follows: PEAR (version 0.9.10) to merge reads, Trimmomatic (version 0.36) to trim low-quality reads, ShortMeRNA (version 2.1) to remove rRNA, and DIAMOND (version 2.0.2) to annotate mRNA data to the RefSeq database [22]
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