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| Sequence Analysis Workshop May 18-22, 2015: http://seqshop.sph.umich.edu/ | | Sequence Analysis Workshop May 18-22, 2015: http://seqshop.sph.umich.edu/ |
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− | Workshop Schedule: [[Media:SeqShopScheduleDec2014.pdf|SeqShopScheduleDec2014.pdf]]
| + | Course Agenda: http://seqshop.sph.umich.edu/index.php/course-agenda |
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| {| class="wikitable" cellpadding=5 | | {| class="wikitable" cellpadding=5 |
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− | ! style="background:#ABE" | Monday !! style="background:#ABE" | Lecture !! style="background:#ABE" | Practical !! style="background:#ABE" | ''Own Genome Analysis'' | + | ! style="background:#ABE" colspan="3"|Monday |
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| + | ! style="background:#ABE" | Lecture !! style="background:#ABE" | Practical !! style="background:#ABE" | ''Own Genome Analysis'' |
− | | [[Media:2014.12_-_Workshop_Introduction.pdf|Brief Introduction and Background]]
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− | | [[Media:Dec2014 SeqShop - Linux.pdf|SeqShop: Practical Intro]]
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− | |rowspan="3" | ''[[SeqShop: Aligning Your Own Genome, December 2014|SeqShop: Aligning Your Own Genome]]''
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| + | | [[Media:2015.05 - Workshop Intro.pdf|Welcome/Design of Human Genetic Studies]] |
− | | [[Media:Sequencing symposium 2014.pptx|Design of Human Genetic Studies]] | + | | [[Media:May2015 SeqShop - Linux.pdf|SeqShop: Quick intro to Linux]] |
− | | | + | |rowspan="2" | ''[[SeqShop: Aligning Your Own Genome, May 2015|SeqShop: Aligning Your Own Genome]]'' |
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− | |
| + | | [[Media:Mapping and assembly May2015.pdf|Sequence Mapping and Assembly]] |
− | | [[Media:Mapping and assemblyDec2014.pdf|Sequence Mapping and Assembly]] | |
| | [[SeqShop: Sequence Mapping and Assembly Practical, May 2015|SeqShop: Sequence Mapping and Assembly Practical]] | | | [[SeqShop: Sequence Mapping and Assembly Practical, May 2015|SeqShop: Sequence Mapping and Assembly Practical]] |
− | [http://iobio.io Live experimentation with IOBIO]
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− | ! style="background:#ABE" | Tuesday !! style="background:#ABE" | Lecture !! style="background:#ABE" | Practical !! style="background:#ABE" | ''Own Genome Analysis'' | + | ! style="background:#ABE" colspan="3" | Tuesday |
| + | |- |
| + | ! style="background:#ABE" | Lecture !! style="background:#ABE" | Practical !! style="background:#ABE" | ''Own Genome Analysis'' |
| + | |- |
| + | | [[Media:seqshop_may_2015_day2_snp_lecture_v2.pdf|Variant Calling and Filtering for SNPs]] |
| + | | [[SeqShop: Variant Calling and Filtering for SNPs Practical, May 2015|SeqShop: Variant Calling and Filtering for SNPs Practical]] |
| + | [http://bam.iobio.io iobio: Visualizing BAM statistics] |
| + | | rowspan="2"|''[[SeqShop: Calling Your Own Genome, May 2015|SeqShop: Calling Your Own Genome]]'' |
| + | |- |
| + | | [[Media:Analysis of SV May2015.pdf|Analysis of Structural Variation - Part 1]] |
| + | [[Media:May2015 Analysis of SV part 2.pdf|Analysis of Structural Variation - Part 2]] |
| + | | [[SeqShop: Analysis of Structural Variation Practical, May 2015|SeqShop: Analysis of Structural Variation Practical]] |
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− | |
| + | ! style="background:#ABE" colspan="3" | Wednesday |
− | | [[Media:seqshop_dec14_day2_snp_lecture_v2.pdf|Variant Calling and Filtering for SNPs]]
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− | | [[SeqShop: Variant Calling and Filtering for SNPs Practical, December 2014|SeqShop: Variant Calling and Filtering for SNPs Practical]]
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− | | rowspan="2"|''[[SeqShop: Calling Your Own Genome, December 2014|SeqShop: Calling Your Own Genome]]''
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| |- | | |- |
− | | | + | ! style="background:#ABE" | Lecture !! style="background:#ABE" | Practical !! style="background:#ABE" | ''Own Genome Analysis'' |
− | | [[Media:Variant Calling and Filtering for INDELs.pdf|Variant Calling and Filtering for INDELs]]
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− | | [[SeqShop: Variant Calling and Filtering for INDELs Practical, December 2014|SeqShop: Variant Calling and Filtering for INDELs Practical]]
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− | ! style="background:#ABE" | Wednesday !! style="background:#ABE" | Lecture !! style="background:#ABE" | Practical !! style="background:#ABE" | ''Own Genome Analysis''
| + | | [[Media:Seqshop 2015 non-SNP variation.pdf|Variant Calling and Filtering for INDELs]] |
| + | [[Media:seqshop_2015_day3_indel_assembly.pdf|More Lessons on Indels + De-novo Assembly Methods]] |
| + | |
| + | | [[SeqShop: Variant Calling and Filtering for INDELs Practical, May 2015|SeqShop: Variant Calling and Filtering for INDELs Practical]] |
| + | |''[[SeqShop: Calling Your Own Genome, May 2015|SeqShop: Calling Your Own Genome]]'' |
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− | |
| + | ! style="background:#ABE" colspan="3" | Thursday |
− | | [[Media:Dec2014 Analysis of SV.pdf|Analysis of Structural Variation - Part 1]]
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− | [[Media:Dec2014 Analysis of SV part 2.pdf|Analysis of Structural Variation - Part 2]]
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− | | [[SeqShop: Analysis of Structural Variation Practical, December 2014|SeqShop: Analysis of Structural Variation Practical]]
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− | |''[[SeqShop: Calling Your Own Genome, December 2014|SeqShop: Calling Your Own Genome]]''
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| |- | | |- |
− | ! style="background:#ABE" | Thursday !! style="background:#ABE" | Lecture !! style="background:#ABE" | Practical !! style="background:#ABE" | ''Own Genome Analysis''
| + | ! style="background:#ABE" | Lecture !! style="background:#ABE" | Practical !! style="background:#ABE" | ''Own Genome Analysis'' |
| |- | | |- |
| + | | [[Media:Stratification.pptx|Estimates of Genetic Ancestry]] |
| + | |[[SeqShop: Estimates of Genetic Ancestry Practical, May 2015| SeqShop: Estimates of Genetic Ancestry Practical]] |
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− | | [[Media:DecWorshop2014-ancestry.pdf|Estimates of Genetic Ancestry]]
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− | |[[SeqShop: Estimates of Genetic Ancestry Practical, December 2014| SeqShop: Estimates of Genetic Ancestry Practical]]
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− | | rowspan="2"|''[[SeqShop: Calling Your Own Genome, December 2014|SeqShop: Calling Your Own Genome]]''
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| |- | | |- |
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| + | | [[Media:Seqshop genetic association analysis 150521.pptx|Genetic Association Analysis]] |
− | | [[Media:Seqshop genetic association analysis 141211.pdf|Genetic Association Analysis]] | + | |[[SeqShop: Association Analysis, May 2015| SeqShop: Association Analysis]] |
− | | | + | | ''[[SeqShop: Calling Your Own Genome, May 2015|SeqShop: Calling Your Own Genome]]'' |
| + | |- |
| + | ! style="background:#ABE" colspan="3" | Friday |
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− | ! style="background:#ABE" | Friday !! style="background:#ABE" | Lecture !! style="background:#ABE" | Practical !! style="background:#ABE" | ''Own Genome Analysis''
| + | ! style="background:#ABE" | Lecture !! style="background:#ABE" | Practical !! style="background:#ABE" | ''Own Genome Analysis'' |
| |- | | |- |
| + | | [[Media:2015.05_-_Workshop_Closing.pdf|Summary]] |
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− | |
| + | |''[[SeqShop: Ancestry On Your Own Genome, May 2015|SeqShop: Ancestry On Your Own Genome]]'' |
− | |[[SeqShop: Genetic Association Analysis Practical, December 2014|SeqShop: Genetic Association Analysis Practical]]
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− | |rowspan="2"|''[[SeqShop: Ancestry On Your Own Genome, December 2014|SeqShop: Ancestry On Your Own Genome]]''
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− | ''[[SeqShop: Calling Your Own Genome, December 2014|SeqShop: Calling Your Own Genome]]''
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| |- | | |- |
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− | | [[Media:2014.12_-_Workshop_Closing.pdf|Example of a Whole Genome Association Study]]
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| |} | | |} |