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-   -   Need help on soap denovo (http://seqanswers.com/forums/showthread.php?t=5086)

sundar 05-11-2010 10:31 PM

Need help on soap denovo
 
Hi all, :confused:

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.

strob 05-12-2010 01:10 AM

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...

sundar 05-12-2010 05:33 AM

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

sundar 05-12-2010 11:05 PM

Quote:

Originally Posted by strob (Post 18416)
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"???????

RGP 11-29-2010 04:03 AM

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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