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  • the low percentage of mapped reads

    Hi all

    I am analyzing RNA-seqs of poplar species generated by Illumia Hi-Seq with the CLC genomic workbench.
    I set the minimum length fraction as 0,7 and minimum similarity fraction as 0,6, Maximum number of hits for a read as 10.
    The mapped reads only take around 70% among all reads.
    Is this percentage too low? Any idea to improve that? BTW, they are paired-end 100 bp reads.

    Thanks!

  • #2
    It sounds OK. The mapping percentage will depend on various things such as read quality, the quality of the reference genome assembly, and properties of the genome itself (repeats, pseudogenes etc).

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    • #3
      Got it, Thanks a lot!

      Comment

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