Advice needed on genomics project

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Advice needed on genomics project

Postby torch5633 » Dec 05 2016 3:46 pm

Dear friends,
I am seeking your opinions on the feasibility of accomplishing the following project within a strict 12-week timeframe.
The challenge is that I have no previous experience to conduct genome assembly and analysis, and even though I have spent numerous hours researching the subject and also personally attended a 4-day workshop at the National Institute of Health (FAES, Trac 45), these efforts have not provided me with enough clues to accomplish the task.

Any comments on how difficult it would be to complete the project within the given time frame would be greatly appreciated. Is it reasonable to expect someone without previous experience or related training in these approaches and tools to accomplish this task within 12 weeks?

Thank you very much.

Assemble, annotate and determine markers and phylogenetic relationships of two R. solani mitochondrial genomes with related fungi and reported R. solani mitochondrial genomes with the following expectations:

A. Prepare a Circular map of two Rhizoctonia solani mitochondrial (mt) genomes (from paired reads of ~26,000,000KB in total size) showing the genes, their position, and on which strand they belong.
B. Find genes with gene names, Open Reading Frames (amino acids sequences), transposons, and introns, etc.
C. Present your results in Figures and Tables.
D. Compare two given mt genomes at the nucleotide level and find selected AG-specific SNPs or INDELs that can be used for rapid diagnostics.
E. Determine the phylogenetic relationships of two mitochondrial genomes with related fungi and reported R. solani mitochondrial genomes.

Re: Advice needed on genomics project

Postby sherke » Dec 13 2016 3:15 pm

You don't define the consequences of missing the deadline. Personally, those are what would drive the decision for me. If the consequences would not be severe and you want to tackle the task, you might well succeed in that time frame. However, given your description of your current abilities, I would not recommend committing to the task if failure would have serious consequences. In your favor, it appears that you would be working with existing data; thus, at least you apparently do not need to learn any actual 'wet-bench' techniques. Even so, with no actual experience in performing the analyses, successfully completing the task in 12 weeks will be challenging at best. It will be particularly challenging if you cannot devote most of your time to the task.
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