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Old 10-29-2010, 08:44 AM   #1
JohnK
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Default 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.
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Old 10-29-2010, 12:48 PM   #2
westerman
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No need for read trimming.
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Old 10-30-2010, 12:40 AM   #3
Chipper
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but you my need to use masks...
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Old 11-02-2010, 10:47 AM   #4
bacdirector
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Default We doubled our mapping by trimming all reads > 35b to 35b

Please see thread in the Bioinformatics forum.

best,

jlw
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Old 11-03-2010, 12:25 AM   #5
hersh
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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...
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