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05-11-2010, 10:31 PM
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#1 |
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Junior Member
Location: india Join Date: May 2010
Posts: 7
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Need help on soap denovo
Hi all,
 Currently i'm running soapdenovo . i am getting two output files one is (1).contig , and the second one is (2).scafseq as per their mentioned in that webpage. But i need to view the result in "GUI" , like any of viewer (for ex: hawkeye , eagleview) . It would be great if i get a positive reply for this Thanks in advance. |
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05-12-2010, 01:10 AM
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#2 |
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Member
Location: Belgium Join Date: Nov 2008
Posts: 79
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Why do you need to view your contigs or scaffolds? As this is a de novo assembly, the only thing you get back are contigs or scaffolds. You can look at them in a special viewer, but you will see nothing more than just doing a "more" or to open them in a text editor...
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05-12-2010, 05:33 AM
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#3 |
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Junior Member
Location: india Join Date: May 2010
Posts: 7
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hmmm ... your right..... But while i done with "velvet" denovo assembly .. I have got the .afg file ,so that i can easily shows the assembly files in the viewer (GUI) format. Like wise in abyss,edena . But while i go for soapdenovo i can get only .contig file in a text format. I Couldn't in view in a GUI ,eventhough i tried some converter like ".toAmos.pl" file to convert .contig to .afg or .ace , There is some problem in a converter..So i am fully confusing ,i couldn't find any of correct path ... it would be great,if i get a solution for this..
Thanks in advance |
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05-12-2010, 11:05 PM
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#4 | |
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Junior Member
Location: india Join Date: May 2010
Posts: 7
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Quote:
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11-29-2010, 04:03 AM
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#5 |
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Junior Member
Location: Italy Join Date: Oct 2008
Posts: 6
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Soap de novo .afg file
Hello Sunder,
to get the.afg you need to tell SoapDeNovo to generate it. In other words you need to turn the amos_file switch on (beware..the .afg it's a LARGE file): ./velvetg output_directory/ -amos_file yes Then you can have a look at it with Tablet or other viewers (beware #2: it will usually take quite a lot of time to generate the .afg output in the GUI viewer). Hope it helps, Rocco |
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