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Old 05-11-2010, 09:31 PM   #1
sundar
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Location: india

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Default 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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Old 05-12-2010, 12:10 AM   #2
strob
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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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Old 05-12-2010, 04:33 AM   #3
sundar
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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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Old 05-12-2010, 10:05 PM   #4
sundar
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Quote:
Originally Posted by strob View Post
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...
Can you tell me the "Special viewer"???????
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Old 11-29-2010, 03:03 AM   #5
RGP
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Default 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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