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# **Pre-interview exercise**
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<span dir="">Before your interview for the Postdoctoral Fellow position we would like you to contemplate a hypothetical data analysis task to show us some of your skills. </span>Please write a short report (less than a page) how you would do the following if you were to be assigned the hypothetical analysis below. In other words,<span dir=""> </span>it is not necessary to download the data and tools if time does not permit, \_we just want to understand<span dir=""> </span>_how you would approach this problem_. The short report is a hypothetical exercise focusing conceptually on how you would perform this analysis.
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<span dir="">Before your interview for the Postdoctoral Fellow position we would like you to contemplate a hypothetical data analysis task to show us some of your skills. </span>Please write a short report (less than a page) how you would do the following if you were to be assigned the hypothetical analysis below. In other words,<span dir=""> </span>it is not necessary to download the data and tools if time does not permit, we just want to understand<span dir=""> </span>_how you would approach this problem_. The short report is a hypothetical exercise focusing conceptually on how you would perform this analysis.
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\-How do you understand the tasks?
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... | ... | @@ -8,23 +8,21 @@ |
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\-What what are the possible alternative choices/tools that you might have available?
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\-If you have time, you can use an R object [here](https://gitlab.svi.edu.au/biocellgen-public/fancm-crossovers-2022/-/tree/master/output/outputR) and make some plots with a brief exploratory analysis. Example code/tutorial can be found [here](https://bioconductor.org/packages/release/bioc/vignettes/comapr/inst/doc/single-sperm-co-analysis.html)
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\-If you have time, you can use an R object [here](https://gitlab.svi.edu.au/biocellgen-public/fancm-crossovers-2022/-/tree/master/output/outputR) and make some plots with a brief exploratory analysis. These R objects are the output of sgcocaller and comapr workflows. Example code/tutorial can be found [here](https://bioconductor.org/packages/release/bioc/vignettes/comapr/inst/doc/single-sperm-co-analysis.html). It is fine to reuse code from the tutorial, but please acknowledge code which has been reused, and explain its purpose in your own words.
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We respect your time and please do not spend more than an hour on this pre-interview exercise. If something is simply too detailed to worry about in a one hour analysis, please skip it.
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Please send the report to wcrismani@svi.edu.au no later than 4pm the day before your interview.
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# **Hypothetical analysis**
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#### (\*\*you do not need to download the raw data and tools if time does not permit. Please just describe how you could attempt it as specified above)
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# **Analysis**
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## <span dir="">Introduction</span>
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<span dir="">Before your interview for the Postdoctoral Fellow position we would like you to complete a small data analysis task to show us some of your skills.</span>
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<span dir="">The task is to conduct a </span>study of meiotic crossover events using bulk whole genome sequencing data from 5 mice (described further below).
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<span dir="">The task is to conduct a </span>study of meiotic crossover events using either the pre-processed bulk whole genome sequencing data or pre-processed single-sperm seqeuncing (described further below).
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<span dir="">We would like you to present a short report (either in a document or notebook) that you will submit ahead of the interview. We may discuss your report in the formal interview or during the day, depending on time</span>.
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<span dir="">We would like you to present a short report (preferably as an R markdown report which includes any code used) that you will submit ahead of the interview. We may discuss your report in the formal interview or during the day, depending on time</span>.
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<span dir="">More specifically, we would like to see:</span>
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... | ... | @@ -37,21 +35,11 @@ Please send the report to wcrismani@svi.edu.au no later than 4pm the day before |
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## The mouse genomic data
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The mice are from what is referred to as a "BC1F1" generation: More specifically previously two inbred mice were crossed from the strains C57BL6 and FVB. The resulting F1 mice were then backcrossed to an FVB inbred, which resulted in the "BC1F1" mice. It is these BC1F1 mice that were sequenced.
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The fastq files, a list of variants, and metadata can be downloaded [here](https://stvincentsinstitute.sharepoint.com/:f:/s/CrismaniData/Ehr5NSEOV-BFl4dWgq8bKrsBmYjCbAlQbDOsEZ9MFFD_Kw?e=vWD06P).
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Fastq files for five mice are provided. Whole genome coverage may be in the range from 1-5x. If this level of coverage is expected to be problematic, please let me know.
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The mice are from what is referred to as a "BC1F1" generation: More specifically previously two inbred mice were crossed from the strains C57BL6 and FVB. The resulting F1 mice were then backcrossed to an FVB inbred, which resulted in the "BC1F1" mice. It is these BC1F1 mice that were sequenced at around 1-5x coverage. Sperm from F1 mice were also sequenced, generally below 1x coverage, and an R object for these is provided too [here](https://gitlab.svi.edu.au/biocellgen-public/fancm-crossovers-2022/-/tree/master/output/outputR)
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## Guidance for the analysis and resources
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It is suggested to perform the detection of crossovers using sgcocaller, unless you are already familiar with another appropriate tool. Documentation and tutorials on the use of sgcocaller can be found at the following two links:
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https://gitlab.svi.edu.au/biocellgen-public/sgcocaller
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https://biocellgen-public.svi.edu.au/hinch-single-sperm-DNA-seq-processing/Crossover-identification-with-sscocaller-and-comapr.html
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Once you have output from sgcocaller, you may can perform some exploratory analysis using [comapr](https://bioconductor.org/packages/release/bioc/html/comapr.html) or any other software that that you find appropriate.
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You may can perform some exploratory analysis using [comapr](https://bioconductor.org/packages/release/bioc/html/comapr.html) or any other software that that you find appropriate.
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Questions to consider:
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... | ... | @@ -61,6 +49,6 @@ Questions to consider: |
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* Do you have enough samples to draw any biological conclusions.
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* How would you approach the _crossover detection_ if in contrast to this experiment which used _genetically identical_ F1s being backcrossed to make BC1F1s, an experiment used multiple _genetically unique_ F4 mice that were interbred to produce F5 pups?
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<span dir="">This task is not meant to be unpleasant or overly onerous. We only expect you to spend 1-2 hours working on it. If you find yourself stuck, feel free to reach out to Wayne for some pointers.</span>
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<span dir="">This task is not meant to be unpleasant or overly onerous. We only expect you to spend an hour working on it. If you find yourself stuck, feel free to reach out to Wayne for some pointers.</span>
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Please send the report to wcrismani@svi.edu.au no later than 4pm the day before your interview. |
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\ No newline at end of file |