Hola
I have a several bacteria which harbor lysogenic viruses (I can induce them with MitomycinC). On one hand side I want to sequence the host. On the other hand side I want to sequence the virus. The host (bacterial) DNA is easy to obtain, however, due to some particularities of the culture media, the virus DNA is very hard to get (at least in a asuficient quantity as required by the sequencing company). That beinng said, I want to do the following:
- sequence the host DNA from an uninduced culture (no viruses present, only bacterial DNA, of a size of 3-4 Mbp genome)
- in paralel, sequence the DNA from an induced culture (both bacterial and viral DNA are present, the viral DNA in 10-30 copies more than the bacterial DNA, but shorter, in between 10-100 kbps).
And of course, I don´t want to do it too expensive. Therefore, I have chosen a MiSeq Illumina package, which will give me about 2.2 mil reads, 300 nt, pair ended (thereore 2x300) per sample.
My question is:
- with this type of sequencing,would I be able to pull appart the viral DNA from the host DNA? My intention is to compare with the virus free bacterial sequences.
- do you thing it would work without sequencing the bacterial host separately, but rather sequencing the infected culture only and then pull appart the bacterial genome from the viral genome?
- with the chosen package - 2.2 mil 2x300 nt reads per sample, do you think I will have a good coverage of the host and viral genomes?
thank you
I have a several bacteria which harbor lysogenic viruses (I can induce them with MitomycinC). On one hand side I want to sequence the host. On the other hand side I want to sequence the virus. The host (bacterial) DNA is easy to obtain, however, due to some particularities of the culture media, the virus DNA is very hard to get (at least in a asuficient quantity as required by the sequencing company). That beinng said, I want to do the following:
- sequence the host DNA from an uninduced culture (no viruses present, only bacterial DNA, of a size of 3-4 Mbp genome)
- in paralel, sequence the DNA from an induced culture (both bacterial and viral DNA are present, the viral DNA in 10-30 copies more than the bacterial DNA, but shorter, in between 10-100 kbps).
And of course, I don´t want to do it too expensive. Therefore, I have chosen a MiSeq Illumina package, which will give me about 2.2 mil reads, 300 nt, pair ended (thereore 2x300) per sample.
My question is:
- with this type of sequencing,would I be able to pull appart the viral DNA from the host DNA? My intention is to compare with the virus free bacterial sequences.
- do you thing it would work without sequencing the bacterial host separately, but rather sequencing the infected culture only and then pull appart the bacterial genome from the viral genome?
- with the chosen package - 2.2 mil 2x300 nt reads per sample, do you think I will have a good coverage of the host and viral genomes?
thank you
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