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11 Cards in this Set
- Front
- Back
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Whole genome shotgun sequencing - general concept
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cut genomic DNA (physical, enzyme or chemical), sequence, if you have large enough pieces, align to reference genome |
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The basic steps in analysis of whole genome resequencing data
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sequence DNA from multiple individuals, align to reference genome and discover variants |
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Sequence capture general idea, reasons you might want to do it instead of whole genome resequencing]
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targeted resequencing reduced cost increase multiplexing while having deep coverage can target enrichment using exome capture |
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What are some problems with targeted resequencing?
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off-target fragments get sequenced not uniform coverage how to deal with genetic uniformity of individuals? |
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RADSeq/ddRAD/GBS - what does each acronym stand for? What is reason to do these techniques instead of whole genome resequencing? What type of data are you trying to discover?
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restriction site associated DNA sequencing, double digest rad, genotype by sequencing these are tools for polymorphisms and are essential for populaiton structure, association mapping, pedigree, QTL, phylogeny |
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What advantage does ddRAD have over GBS/RAD?
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cheap/simple libreary construction eliminate random shearing and end repair size selection |
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Bisulfite sequencing - what is the purpose? How does it work? What problems often arise from bisulfite treatment
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lets you know where methylation occurs in DNA by transforming methylated cytosine to uracil often inaccurate/misses target, DNA can degreade during bisulfite treatment |
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Sequence assembly - what are some factors that increase difficulty
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size repetiveness polyploidy heterzygosity |
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Contig vs scaffold in assembly terms
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? |
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Steps of sequence assembly workflow
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quality assessment trimming quality assessment map to reference visualization call variants assess function of variants submit to SRA |
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What is N50 statistic?
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The length for which a collection of contigs of that length or longer contains at least 50% |
