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- Mapped read data evaluation (SAMtools)
- Installing and compiling tools on Unix
- Integrated pipeline for microbial genome re-sequencing analysis (breseq)
- Calling variants in multiploid genomes and mixed populations (FreeBayes)
- Practical advice about some things to watch out for with short read re-sequencing data
- UCSC genome browser & GEO/, SRA data downloads - 30 min - Anna
- 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 Anna Scott
- Comparing variants across samples (VCFtools) annovar/snpeff/plink/vaast/qiime Dhivya & Scott shell/perl/python scripting – candidates for recessive disease
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- Differential gene expression analysis
- Splice variant analysis
<break> - non-coding RNA analysis 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?)
Day 4: Assembly
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