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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.
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https://stvincentsinstitute.sharepoint.com/:f:/s/everything/EhsB8UYRrChOiTjyCtUBV-UB1KddW9d0XXKe4SdCzZQr_Q?e=1b0kYd
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The fastq files, a list of variants, and metadata can be downloaded [here](https://stvincentsinstitute.sharepoint.com/:f:/s/everything/EhsB8UYRrChOiTjyCtUBV-UB1KddW9d0XXKe4SdCzZQr_Q?e=1b0kYd).
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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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... | ... | @@ -33,7 +31,7 @@ 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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It is _critical_ that sgcocaller is bun in "bulk" mode in order to execute correctly.
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It is _critical_ that sgcocaller is run in "bulk" mode in order to execute correctly.
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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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... | ... | @@ -41,8 +39,9 @@ Questions to consider: |
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* What is the expected crossover frequency?
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* How confident are you in the output of sgcocaller?
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* A common fault of crossover analyses are 'dubious' close double crossovers that are only supported by a limited number of variants, that are perhaps all in the same read. In other words, reads that are mapped to regions that are not the true genomic location of the read's origin.
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* A common fault of crossover analyses are 'dubious' close double crossovers that are only supported by a limited number of variants, that are perhaps all in the same read. In other words, reads that are mapped to regions that are not the true genomic location of the read's origin. Are there any dubious close double crossovers in these sgcocaller output?
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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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