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  • how to treat read-through in mapping for differential expression analysis

    hi all
    I got 2x150 reads that I used to perform denovo assembly using Trinity, with Trimmomatic option on. Problem is, that nearly 35-40% of reads of all 6 libraries resulted with read-through (Trimmomatic retained forward read only). For assembly that was not a problem, but now I am unsure how to use such libraries to perform differential expression analysis to look for DEGs.
    Very thankful to anyone who can give me suggestions
    Marco

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