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I did RNAseq of a Drosophila cell line. By using RNASTAR in Galaxy I am getting high number of reads mapped to too many loci. (uniquely mapped 60 %, mapped to multiple loci 10 %, mapped to too many loci 24 %). Later when I am doing FeatureCounts there is only 40 % assigned, unasigned : unmapped 20 %, unassigned : mapping quality 35 %. Should I consider this as a bad result or is it a problem of cell culture?