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Old 04-23-2009, 11:41 PM   #1
nilshomer
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Default SAMTOOLs tview for ABI color space

I have a working patch to view ABI SOLiD color space using samtools (http://samtools.sourceforge.net/) text viewer. For example, some of the features using output from BFAST (in SAM format), which includes the "CS" and "CQ" tags, are:

- option to display colors instead of nucleotides.
- option to color bases/colors based on color. This is similar if you want to color bases based on the given base.
- option to color bases/colors based on color quality.
- the "." (dot) option when displaying color space will only show those colors that were corrected during alignment (i.e. the color errors).
- option to remove all insertions in the current display (in some regions, spurious insertions can cause a headache when viewing that region).

PM me and I can supply you with a source version.

Nils
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Old 07-05-2010, 03:18 AM   #2
KevinLam
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neat!
Please send me a copy?
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Old 07-05-2010, 07:15 AM   #3
nilshomer
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Quote:
Originally Posted by KevinLam View Post
neat!
Please send me a copy?
It is now included in samtools. You can use the "c" option to change to color space.
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