where is the parameter --min_kmer_cov ?

[曾玺]

Dear authors,

I can't run trinity due to too large size of data set. And I learned that it can reduce the memory Trinity --min_kmer_cov  requirements with large read sets for the manual of Trinity(https://trinityrnaseq.github.io/advanced_trinity_guide.html). But I find this parameter is not existing in trinityrnaseq-2.0.6. Could you please tell me how can I get it ?

Best regards,

Michael

[Mark Chapman]

Hi Michael,
It is there, you just add it to the list of parameters. See the supplementary info for the Nature Methods paper for more details.
Typically for the nice situation of 'too much data', normalisation is the best way to proceed. You can do this separately before running the rest of trinity or just add the normalise flag to the command line.
Best wishes, Mark

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[曾玺]

Hi Mark,

Thanks a lot for your help. I will try soon.

Best,

Michael

在 2015年9月21日星期一 UTC+8上午4:51:29，Mark Chapman写道：

Hi Michael,
It is there, you just add it to the list of parameters. See the supplementary info for the Nature Methods paper for more details.
Typically for the nice situation of 'too much data', normalisation is the best way to proceed. You can do this separately before running the rest of trinity or just add the normalise flag to the command line.
Best wishes, Mark

On 20 Sep 2015 17:29, "曾玺" <zengx...@gmail.com> wrote:

Dear authors,

I can't run trinity due to too large size of data set. And I learned that it can reduce the memory Trinity --min_kmer_cov  requirements with large read sets for the manual of Trinity(https://trinityrnaseq.github.io/advanced_trinity_guide.html). But I find this parameter is not existing in trinityrnaseq-2.0.6. Could you please tell me how can I get it ?

Best regards,

Michael

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