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Old 08-03-2011, 07:17 AM   #1
lei
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Default how to trim solid reads length?

are there any tools available to trim solid reads length? for example, I want to extract first 30bp.
Thanks!
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Old 08-03-2011, 07:33 AM   #2
westerman
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No tools that I know of. Both Emboss and Galaxy do not seem to have a way (although there are so many programs in both that it is hard to tell.) Trimming is trivial to do in perl or another language. If you are a "layer 3" bioinformatics person (see http://www.homolog.us/blogs/?p=85) then it will take less time to write the program than to respond back to this message. :-)
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Old 08-03-2011, 10:33 AM   #3
lei
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OK, I wrote one, but not so fast, that's why I ask here to check whether there is some tool to do it already.
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Old 08-03-2011, 11:48 AM   #4
gringer
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I've managed to do it by double-encoding, passing through the fastx-toolkit, then reversing the double-encoding.
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Old 12-13-2012, 03:58 PM   #5
carmeyeii
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Are there any new ways to do this?
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Old 12-13-2012, 04:37 PM   #6
gsgs
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I don't understand. "trim" = cut ? zurechtstutzen
Nor do I know/understand Emboss,Galaxy,layer 3,
double-encoding,fastx.
I just feel, there must be something wrong with bioinformatics,
if cutting the length of a sequence gets a thread here.
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Old 12-13-2012, 08:47 PM   #7
gringer
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Quote:
Originally Posted by gsgs View Post
I just feel, there must be something wrong with bioinformatics,
if cutting the length of a sequence gets a thread here.
Let's reiterate what westerman said:

Quote:
Originally Posted by westerman
Trimming is trivial to do in perl or another language.... it will take less time to write the program than to respond back to this message.
Or, for that matter, reading through all the posts in this thread, then asking if anyone has thought up their new favourite way to trim reads to a particular length.
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Old 12-14-2012, 07:55 AM   #8
carmeyeii
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Lovely

Cheers.
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