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Old 03-22-2010, 04:55 PM   #1
bawee
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Location: Australia

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Default Breakdancer options

Could anyone please enlighten me on the right format to specify options for BreakDancerMax?

I've tried various ways of putting up options for BreakDancerMax:

% BreakDancerMax.pl config.list -o -e -r 10 > brd1.out

% BreakDancerMax.pl -o -e -r 10 config.list > brd1.out

and even tried putting them into the config file.

None of these seem to respond by giving an output with a minimum read count of 10 for each SV (-r 10).


Thanks.
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Old 03-23-2010, 10:37 AM   #2
pickw
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In your command line example,
% BreakDancerMax.pl -o -e -r 10 config.list > brd1.out

You need to specify a chromosome after the "-o", e.g. "-o 1" or "-o
chr1" depending on how you named your reference sequences.

-Ken
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Old 03-23-2010, 04:25 PM   #3
bawee
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Thanks Ken,

I am working on a bacterial genome so there is only one chromosome. I thought therefore I would leave the option as default (ie. all chromosomes).
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Old 03-23-2010, 06:01 PM   #4
bawee
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Hi Ken,

I've tried putting the reference id in my command and it give the output I expect it to. Thanks for that!
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