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Old 03-04-2011, 07:31 AM   #1
gstitan
Junior Member
 
Location: Essonne

Join Date: Oct 2009
Posts: 7
Default Metasim 454 data paired ??

I try to generate paired data 454 with Metasim0.9.5 but it desn't work!
No error is producted by Metasim but in output file, it's only single read which are generated.

My command line:
MetaSim cmd -4 --454-paired-read-length 400 --454-mate-probability 1 -r29000 -d output.fasta -z genome.fasta

I obtain this type of output:
>r1.1
>r2.1
>r3.1
...

I should obtain :
>r1.1
>r1.2
>r2.1
>r2.2
...

Someone can help me?

Thanks
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Old 03-04-2011, 09:03 AM   #2
kmcarr
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Location: USA, Midwest

Join Date: May 2008
Posts: 1,155
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MetaSim has written the 454 mate-paired sequence in the way that the 454 software would do it, and the way that it is generated by the instrument. A single read containing both of the mate pairs with a 44bp linker in between the reads. To get the output you expected you have to add the option --454-remove-linker to your command.
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Old 03-07-2011, 12:37 AM   #3
gstitan
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Thanks kmcarr!
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