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  • piemmea
    Junior Member
    • Mar 2013
    • 6
    #1

    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
    Tags: differential analysis, read-through, rnaseq analysis, trimmomatic
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