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  • Read trimming- color space

    Any ABI-recommended programs for read-trimming? I understand it might not be necessary due to the nature of BioScope's mapping software. Thank you.

  • #2
    No need for read trimming.

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    • #3
      but you my need to use masks...

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      • #4
        We doubled our mapping by trimming all reads > 35b to 35b

        Please see thread in the Bioinformatics forum.

        best,

        jlw

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        • #5
          You can look at quality values of the reads. If you see drastic drop down in quality values at the end of every reads , you can trim reads by several bases....which should increase mapping... If you use corona_lite for mapping there is an option of masking several positions during mapping...

          Bioscope mapping is seed based , so even if you dont trim , reads will still map the reference...

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