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- Mapped read data evaluation (SAMtools)
- Installing Linux tools
- Identifying mutations in microbial genomes (breseq)
- Genome variation in mixed populations (FreeBayes, deepSNV)
- Practical advice - short read re-sequencing data
- Calling variants in diploid genomes
- Structural variation
- SRA toolkit, UCSC Genome Browser
- Variant calling with GATK (use their wiki), more detail on .vcf format, look at Human data 1000 genome VCF files and describe how to access 1000 genome data
- Annotating variants annovar/snpeff/plink/vaast/qiime Dhivya & Scott shell/perl/python scripting – candidates for recessive disease
Day 3: RNA-seq
- Differential gene expression analysis
- Splice variant analysis
<break> - non-coding RNA analysis annotation - unique mapping (shrimp/grep), miRNA’s abundance/editing, other: snoRNA, snRNA, lincRNA, piRNA, tRNA, degradome, etc. etc. (not poly-A; not annotated)
- Transcriptome assembly & annotation velvet/oases, TrinityRNAseq; BLAST, GOminer, (ELI?)
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