1. | Ab initio assembly with short reads. | Uses a hashing technique to index the genome.It can find alignments with as many as 2 mismatches Uses Mate-pairs Also takes advantage of the Qscore information to only use reads which are likely to be correct. | ||
2. | Detecting variation with short readsAlgorithms: PolyBayes, PyroBayes, SHRimp | 1.De novo assembly for short reads: review 2.Probability that read starts at a position: Uniform distribution 3.Overlap fraction and relationship to the Lander-waterman equations |
||
3. | Structural variation in clone-end dataStructural variations in the human genomeMethods for detecting structural variations. | 1. Focus of the paper is detecting large-scale structural variations of genes. 2. Critical questions I had initially: - What about variations outside of the gene context? - Can these methods be used to find small rearrangements / indels? - What is the lower size limit? |
||
4. | microRNAs.Next generation data storage issuesCompressed sequence alignment | 1. Recall how reads are stored 2. Multiple Users of NGS data? 3. Compressing read data |
||
4. | microRNAs.Next generation data storage issuesCompressed sequence alignment | 1. Recall how reads are stored 2. Multiple Users of NGS data? 3. Compressing read data |
||
5. | The transcriptomeGene Expression ProfilingDe novo transcriptome sequencing | 1. To catalog all species of RNA transcripts 2. To determine the transcriptional structure of genes, including: - 5’ end, 3’ end, splicing patterns, and modifications 3. To quantify the changes in expression levels of individual transcripts during cellular development and under different conditions. |
||
6. | Basics of designing a microarrayImage analysisNormalizationClusteringMicroarray databases | 1. Competitive hybridization 2. Indirect measurements |
||
7. | R for analyzing microarray data.Microarray methods for copy number variation. | 1. Installing Bioconductor 2. Affymetrix arrays 3. Getting microarray data into bioconductor |