Difference between revisions of "SeqShop: May 2015"

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{| class="wikitable" cellpadding=5
 
{| class="wikitable" cellpadding=5
 
|-
 
|-
! style="background:#ABE" | Monday !! style="background:#ABE" | Lecture !! style="background:#ABE" | Practical !! style="background:#ABE" | ''Own Genome Analysis''
+
! style="background:#ABE" colspan="3"|Monday
 
|-
 
|-
|
+
! style="background:#ABE" | Lecture !! style="background:#ABE" | Practical !! style="background:#ABE" | ''Own Genome Analysis''
| [[Media:2014.12_-_Workshop_Introduction.pdf|Brief Introduction and Background]]
+
|-
| [[Media:Dec2014 SeqShop - Linux.pdf|SeqShop: Quick intro to Linux]]
+
| [[Media:2015.05 - Workshop Intro.pdf|Welcome/Design of Human Genetic Studies]]
|rowspan="3" | ''[[SeqShop: Aligning Your Own Genome, December 2014|SeqShop: Aligning Your Own Genome]]''
+
| [[Media:May2015 SeqShop - Linux.pdf|SeqShop: Quick intro to Linux]]
 +
|rowspan="2" | ''[[SeqShop: Aligning Your Own Genome, May 2015|SeqShop: Aligning Your Own Genome]]''
 
|-
 
|-
|
+
| [[Media:Mapping and assembly May2015.pdf|Sequence Mapping and Assembly]]
| [[Media:Sequencing symposium 2014.pptx|Design of Human Genetic Studies]]
 
 
| [[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]]
 
|-
 
|-
|
+
! style="background:#ABE" colspan="3" | Tuesday
| [[Media:Mapping and assemblyDec2014.pdf|Sequence Mapping and Assembly]]
 
|  [http://bam.iobio.io iobio: Visualizing BAM statistics]
 
 
|-
 
|-
! style="background:#ABE" | Tuesday !! 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:seqshop_may_2015_day2_snp_lecture_v2.pdf|Variant Calling and Filtering for SNPs]]
| [[Media:seqshop_dec14_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]]
 
| [[SeqShop: Variant Calling and Filtering for SNPs Practical, May 2015|SeqShop: Variant Calling and Filtering for SNPs Practical]]
| rowspan="2"|''[[SeqShop: Calling Your Own Genome, December 2014|SeqShop: Calling Your Own Genome]]''
+
[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:Dec2014 Analysis of SV.pdf|Analysis of Structural Variation - Part 1]]
+
[[Media:May2015 Analysis of SV part 2.pdf|Analysis of Structural Variation - Part 2]]
[[Media:Dec2014 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]]
 
| [[SeqShop: Analysis of Structural Variation Practical, May 2015|SeqShop: Analysis of Structural Variation Practical]]
 
|-
 
|-
! style="background:#ABE" | Wednesday !! style="background:#ABE" | Lecture !! style="background:#ABE" | Practical !! style="background:#ABE" | ''Own Genome Analysis''
+
! style="background:#ABE" colspan="3" | 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:Variant Calling and Filtering for INDELs.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: Variant Calling and Filtering for INDELs Practical, May 2015|SeqShop: Variant Calling and Filtering for INDELs Practical]]
|''[[SeqShop: Calling Your Own Genome, December 2014|SeqShop: Calling Your Own Genome]]''
+
|''[[SeqShop: Calling Your Own Genome, May 2015|SeqShop: Calling Your Own Genome]]''
 +
|-
 +
! style="background:#ABE" colspan="3" | Thursday
 
|-
 
|-
! 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]]
| [[Media:DecWorshop2014-ancestry.pdf|Estimates of Genetic Ancestry]]
 
 
|[[SeqShop: Estimates of Genetic Ancestry Practical, May 2015| SeqShop: Estimates of Genetic Ancestry Practical]]
 
|[[SeqShop: Estimates of Genetic Ancestry Practical, May 2015| SeqShop: Estimates of Genetic Ancestry Practical]]
 
|
 
|
 
|-
 
|-
|
+
| [[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: 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
 
|-
 
|-
! 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]]
 
|
 
|
| [[Media:2014.12_-_Workshop_Closing.pdf|Example of a Whole Genome Association Study]]
+
|''[[SeqShop: Ancestry On Your Own Genome, May 2015|SeqShop: Ancestry On Your Own Genome]]''
|
 
|rowspan="2"|''[[SeqShop: Ancestry On Your Own Genome, December 2014|SeqShop: Ancestry On Your Own Genome]]''
 
 
|-
 
|-
 
|}
 
|}

Latest revision as of 10:40, 22 May 2015

Sequence Analysis Workshop May 18-22, 2015: http://seqshop.sph.umich.edu/

Course Agenda: http://seqshop.sph.umich.edu/index.php/course-agenda


Monday
Lecture Practical Own Genome Analysis
Welcome/Design of Human Genetic Studies SeqShop: Quick intro to Linux SeqShop: Aligning Your Own Genome
Sequence Mapping and Assembly SeqShop: Sequence Mapping and Assembly Practical
Tuesday
Lecture Practical Own Genome Analysis
Variant Calling and Filtering for SNPs SeqShop: Variant Calling and Filtering for SNPs Practical

iobio: Visualizing BAM statistics

SeqShop: Calling Your Own Genome
Analysis of Structural Variation - Part 1

Analysis of Structural Variation - Part 2

SeqShop: Analysis of Structural Variation Practical
Wednesday
Lecture Practical Own Genome Analysis
Variant Calling and Filtering for INDELs

More Lessons on Indels + De-novo Assembly Methods

SeqShop: Variant Calling and Filtering for INDELs Practical SeqShop: Calling Your Own Genome
Thursday
Lecture Practical Own Genome Analysis
Estimates of Genetic Ancestry SeqShop: Estimates of Genetic Ancestry Practical
Genetic Association Analysis SeqShop: Association Analysis SeqShop: Calling Your Own Genome
Friday
Lecture Practical Own Genome Analysis
Summary SeqShop: Ancestry On Your Own Genome