kmerFreq

[Radhika Khetani]

Hi,

Could someone elaborate on how the information about kmer frequency that is in the ".kmerFreq" file is gathered during the pregraph phase of SOAPdenovo? 

I would like to interpret an unexpected result that came out of a pregraph run I did using 20x data (genome size is a rough estimate) and a kmer size of 17 (-K 17). See attached image for the plot; as you can see the peak is at 6x or 7x which is suggesting a larger genome size. But, could there be another explanation? An issue with ploidy or heterozygosity? I would appreciate any thoughts on this matter.

Best,

Radhika

[谢寅龙]

Hi Radhika,

Not sure how you estimated the genome size, if based on allied species, I think it's ploidy.

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发件人: bgi-...@googlegroups.com [bgi-...@googlegroups.com] 代表 Radhika Khetani [khet...@gmail.com]
发送时间: 2013年2月5日 3:15
到: bgi-...@googlegroups.com
主题: [BGI-SOAP:676] kmerFreq

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[刘兵行]

Radhika, I think you can show more information, including read length, estimated genome size, total sequencing data. 

If possible, you can run kmerfreq in coperead.sf.net to calculate a new curve. You just need to pay attention to the parameter -c to filter the low quality kmers.

Best!

Binghang

2013/2/20 谢寅龙 <xi...@genomics.cn>

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[Manoj Samanta]

Radhika,

Please do not forget another possibility - too many duplicate reads.

Manoj

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