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Old 04-15-2009, 03:27 AM   #1
jordi
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Location: València, Spain

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Default what's clipping point?

Hi!
I'm working with de novo 454 data and , after a GS FLX asemmbly, I try to see the results with clview which works with .ace files and I can see something like the attachment file. The reads have right and left clip. What does it mean? I found anything about this clipping point. Can I change some value in order to improve the assembly?
Thank you very much!
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File Type: png assembly1.png (64.4 KB, 38 views)
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Old 05-26-2009, 01:47 AM   #2
flxlex
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Default

Reads are quality trimmed before assembly, the new start and stop are the left and right clipping points. Usually, the left (5') side is never trimmed (beyond the first four bases that are common for all reads).

Trim values can be changed using the sfffile command, check the manual.
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