Hi. I am new. I have Just graduated and have to start an internship. When I Will start I already have a task to perform and I would like to ask you what do you think are the analysis I should perform in order to answer their questions. They have a colture of a bacteria and they extracted the DNA and performed 4 different sequencing analysis.
1. Sequencing with Illumina 2. Sequencing with Nanopore 3. Performed whole genome amplification then sequencing with Illumina 4. Performed whole genome amplification then sequencing with Nanopore.
MY JOB IS TO analyse the sequencing data and to tell them Which One Is Better, if Nanopore or Illumina with the whole genome amplification.
The reason they perform whole genome amplification is because this colture grows really really slow and they never have the amount of needed DNA to directly perform Illumina or Nanopore. This Is a test they perform not on their bacteria of interest but with a pure colture they already have...but After this step when they have the data they Will
And the most importante Is to see if the WHOLE GENOME AMPLIFICATION KEEP THE PLASMIDS or make It to lose them in the process.
They want to try the whole genome amplification because the amount of DNA Is very very low and the colture takes months to grow. They want me to tell them if this Is a good alternative to increase the amount of DNA for sequencing.
MY questione Is: what are the analysis you think I would have to perform with this 4 data they gave me? What should I do to see PLASMID Lost and others in the data from pre- whole genome amplification compared tot the sequencing without amplification?
(I was thinking at sequencing quality - fastqc to see Infos about the sequencing itself but what about PLASMID Lost?)
I really Hope you could answer. Thank you!
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