[BGI-SOAP:171] SOAPdenovo paired-end cutoff values

[Waldo]

Hi all,
I am using SOAPdenovo v1.04 for Linux (64bit). I have tried to adjust
the parameter "pair_num_cutoff" down to 2 for short-insert libraries
and down to 3 for long-insert libraries from their default settings of
3 and 5, respectively, in my configuration file. However, when I run
the scaffolding algorithm, the default settings of 3 and 5 are used as
reported in the output. Has anyone else tried to adjust this setting,
and does anyone know if the default settings are also the minimum
values accepted?

Thanks,
Kim

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[Oksana Riba]

Hello,

I tried raising the value of pair_num_cutoff to 5 and to 10, but it did not change the final scaffolds. I have checked the log file and it states that "Cutoff for number of pairs to make a reliable connection: 3", which is the default value.

Cheers,

Oksana

[honghe sun]

I met this problem too. Is there anyone know how to fix it? 

Thanks! 

Best,

Honghe