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  • ht seq counting/ Most of reads into alignment non unique

    Hi all,

    I am new to Rna seq. I am runnign ht seq within galaxy but at the end most of my reads end up in alignment non unique

    so the parameter im using for ht seq are
    mode : union
    strandness: reverse
    feature type : gene
    Im using a gff file from gencode (human)

    _no_feature 1029187
    __ambiguous 998628
    __too_low_aQual 0
    __not_aligned 0
    __alignment_not_unique 13419757


    I have single end read , 75 bp

    I am trying to understand why most of the reads are in alignment non unique. Also im not sure if featrure type set to gene would give exoninc and intronic reads as im interested in both.

    thank you in advance

    Best,
    Mirjam

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