Hi all,
we are looking to buy our first NGS machine for our lab to use from the beginning of 2012 and I am in charge of recommending a suitable machine for our needs. We work with human genome and cytogenetics in my lab.
We have a limited budget and our idea is to get Illumina' s MiSeq (we are also considering Roche GS Junior System but we are leaning towards miSeq).
As I come from a computer scientist background and its the first time I venture into the NGS machines world (before i was only in the analysis part) I have a few questions and would be grateful if anyone could answer or direct me to somewhere to read:
1. One of the aplications we will want to do is exome sequencing. I have read that miseq is not able to do whole genome sequencing unless we are talking about a very small genome. What about the exome? Can I use the TruSeq Exome Enrichment kit with the DNA sample preparation kit and prepare out libraries and sequence on MiSeq?
2. I read in this forum that for 1 GB MiSeq can produce 2x 150 bp reads and that for a 50Mb exome capture that would be 20x coverage. Can someone explain to me how these numbers are calculated? How do I know, given a capture library of X Mb and say I want to sequence paired end reads of 150 bp each, how much coverage I will get? Also, If i want to have say at least an average of 50x coverage in each position of the exome, how do i calculate how much data i need and the length of reads i should put miSeq to produce for best outcome? Could you direct me to a publication or something I can read to clear these notions and numbers in my head because i need to understand them to be able to assess NGS machines?
3.Can I create libraries of differents parts of the exome to be resequenced by miSeq so I can have a better coverage at each position?
4. Does anyone know the cost of miSeq machine and how much a single run will cost?
Thank you in advance
we are looking to buy our first NGS machine for our lab to use from the beginning of 2012 and I am in charge of recommending a suitable machine for our needs. We work with human genome and cytogenetics in my lab.
We have a limited budget and our idea is to get Illumina' s MiSeq (we are also considering Roche GS Junior System but we are leaning towards miSeq).
As I come from a computer scientist background and its the first time I venture into the NGS machines world (before i was only in the analysis part) I have a few questions and would be grateful if anyone could answer or direct me to somewhere to read:
1. One of the aplications we will want to do is exome sequencing. I have read that miseq is not able to do whole genome sequencing unless we are talking about a very small genome. What about the exome? Can I use the TruSeq Exome Enrichment kit with the DNA sample preparation kit and prepare out libraries and sequence on MiSeq?
2. I read in this forum that for 1 GB MiSeq can produce 2x 150 bp reads and that for a 50Mb exome capture that would be 20x coverage. Can someone explain to me how these numbers are calculated? How do I know, given a capture library of X Mb and say I want to sequence paired end reads of 150 bp each, how much coverage I will get? Also, If i want to have say at least an average of 50x coverage in each position of the exome, how do i calculate how much data i need and the length of reads i should put miSeq to produce for best outcome? Could you direct me to a publication or something I can read to clear these notions and numbers in my head because i need to understand them to be able to assess NGS machines?
3.Can I create libraries of differents parts of the exome to be resequenced by miSeq so I can have a better coverage at each position?
4. Does anyone know the cost of miSeq machine and how much a single run will cost?
Thank you in advance
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