Hi,
Do anybody mind to share that what is the "best" or "suitable" input file for genome size estimation program such as Jellyfish?
I still confuse should I used original raw sequencing read, pair-end data after preprocessing analysis (trim adaptor, remove low quality read, remove duplicate read, etc), or pair-end + single-end data after preprocessing analysis (trim adaptor, remove low quality read, remove duplicate read, etc)?
I have try the above 3 different data as an input file for Jellyfish by using 17-mer.
My data set is novel isolated bacteria.
Thus I not too sure what is the exact genome size.
The peak of 17-mer frequency (M) in reads is correlated with the real sequencing depth (N), read length (L), and kmer length (K), their relations can be expressed in a experienced formula: M = N * (L – K + 1) / L.
All the above 3 different data set gives me different peak of 17-mer frequency.
Thus it effect the calculation of genome size too.
Thanks for any advice.
Do anybody mind to share that what is the "best" or "suitable" input file for genome size estimation program such as Jellyfish?
I still confuse should I used original raw sequencing read, pair-end data after preprocessing analysis (trim adaptor, remove low quality read, remove duplicate read, etc), or pair-end + single-end data after preprocessing analysis (trim adaptor, remove low quality read, remove duplicate read, etc)?
I have try the above 3 different data as an input file for Jellyfish by using 17-mer.
My data set is novel isolated bacteria.
Thus I not too sure what is the exact genome size.
The peak of 17-mer frequency (M) in reads is correlated with the real sequencing depth (N), read length (L), and kmer length (K), their relations can be expressed in a experienced formula: M = N * (L – K + 1) / L.
All the above 3 different data set gives me different peak of 17-mer frequency.
Thus it effect the calculation of genome size too.
Thanks for any advice.