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Old 08-15-2013, 08:46 AM   #1
pmgr
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Location: Sweden

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Default order scaffolds

There is a genome in unoriented and unorder scaffolds. I am interested in a specific area of the genome. Therefore I managed to align the scaffolds to a closely related species and I got an idea about the orientation of the scaffolds.

I want to visualize it in a genome browser in the correct order.
Any idea how to modify the orientation inside the genbank file of those scaffolds?

Any help please`?
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Old 08-16-2013, 07:48 AM   #2
SES
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The ABACUS program was designed for this purpose and I have found it to work quite well. ABACUS is a part of the PAGIT pipeline, which includes other programs that you may find useful.
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Old 08-17-2013, 06:23 AM   #3
maubp
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Here's a duplicate question on BioStars,
http://www.biostars.org/p/79104/

Here's an older BioPerl answer http://www.biostars.org/p/43236/
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