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Old 02-16-2010, 06:59 AM   #1
javijevi
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Default Converting nucleotide-space to color-space

Does anybody know where could I find a tool to convert a nucleotide-space sequence to a color-space sequence?

Thanks a lot in advance,
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Old 02-16-2010, 08:45 AM   #2
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Originally Posted by javijevi View Post
Does anybody know where could I find a tool to convert a nucleotide-space sequence to a color-space sequence?
I've found such a tool in the bin directory of Corona_Lite distribution. Its name is encodeFasta.py. It could be used for several interconversions (color-space, double-encoded, nucleotide-space).

One caveat is that nucleotides to be converted to color-space must be all uppercase.

Any experience with this tool?

Any other similar tool?
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Old 02-17-2010, 07:38 AM   #3
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Aside from the mentioned need for capital letters plus a requirement for only ACGTN the encodeFasta.py program works fine. Validate your sequence using reference_validation.pl first. Why ABI did not combine these two programs into one ... well, that is water under the bridge. People really should be using Bioscope instead of Corona Lite.
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Old 09-20-2010, 01:36 AM   #4
Temima
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From what I can make out, when working with base sapace, encodeFasta.py can only convert to double encoded. What do I do if I want my nucleotide data in actual color space format?
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Old 09-20-2010, 02:15 AM   #5
zee
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Originally Posted by westerman View Post
. People really should be using Bioscope instead of Corona Lite.
If Bioscope were more readily available. Now it has been moved to a cloud-based pay-to-use service. That's not useful for those of us who already have computing infrastructures.
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Old 09-20-2010, 04:46 AM   #6
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If Bioscope were more readily available. Now it has been moved to a cloud-based pay-to-use service. That's not useful for those of us who already have computing infrastructures.
I am not aware that Bioscope is exclusively on the cloud. Certainly I am running the latest on our own hardware.

The solidbioscope.com cloud option at $1900/month looks like it would handle the processing of a single SOLiD machine with some wiggle room for extra needs.

As for availability you can download bioscope from a web site so, in my mind, it becomes rather easy to get. You may have to ask your LifeTech representative for the web site address. Also it may be true that Bioscope will cost something -- or perhaps not. We get it for free and can, as far as I know, let our customers run the software. But that may because we own a SOLiD and thus the cost, if any, may be part of our instrument's annual maintenance fee.
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Old 09-20-2010, 05:03 AM   #7
westerman
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Originally Posted by Temima View Post
From what I can make out, when working with base sapace, encodeFasta.py can only convert to double encoded. What do I do if I want my nucleotide data in actual color space format?
encodeFasta can go to and from base-space to color-space and vice-versa. It can go from base-space to double-encoded and vice-versa. Look at the command line parameters '-n' and '-d'. Or in your case the not using those parameters.
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Old 11-29-2010, 02:14 AM   #8
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a belated huge thank you westerman!
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