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.
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No need for read trimming. -
but you my need to use masks...Comment
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We doubled our mapping by trimming all reads > 35b to 35b
Please see thread in the Bioinformatics forum.
best,
jlwComment
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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...Comment
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