Hi,
How to estimate the bacterial genome size (GC rich) when there was no close reference genome ?
At first i tried jellyfish and generated the histogram plots (for all the avail kmers) and here the exact peak (what i guess) were identifed and calculated, but i am only getting less than half (too less ) off the genome size when compared to generated assemly produce from soapdenovo2.
And then i tried kmergenie (for all different kmers) same i am not getting proper estimation..
* Illumina hiseq : Paired end data : Read length 100bps ;
* GC perecent : 63 % ; (Read_1)
* Duplicates in fastq : ->48% (Read_1)
* Read_1 :10128605 (data from FastQC)
Any Suggestions could be really greatfull..
Thank you very much..
How to estimate the bacterial genome size (GC rich) when there was no close reference genome ?
At first i tried jellyfish and generated the histogram plots (for all the avail kmers) and here the exact peak (what i guess) were identifed and calculated, but i am only getting less than half (too less ) off the genome size when compared to generated assemly produce from soapdenovo2.
And then i tried kmergenie (for all different kmers) same i am not getting proper estimation..
* Illumina hiseq : Paired end data : Read length 100bps ;
* GC perecent : 63 % ; (Read_1)
* Duplicates in fastq : ->48% (Read_1)
* Read_1 :10128605 (data from FastQC)
Any Suggestions could be really greatfull..
Thank you very much..
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