4 Which aligner is best? What type of data do you have? What is your research question?
5 Methods of alignment Splice awareness: What will be matched first? Splice unaware (Bowtie, BWA)FasterSplice aware (Tophat, MapSplice, SpliceMap)SlowerYields more information on splice junctionsWhat will be matched first?Whole genome?Known transcriptome?A short segment of each read first?
6 Why tophat? Popular Splice aware de novo or sequenced genome modes Transcriptome or whole genome assemblyLots of options for customizationDrawbacksLots of parameters to set & optimize
7 Tophat2 – how does it work? Kim et al., 2013 Genome Biology
14 I have included an example script for Script05_makeBrowserTracks.shRequires bedGraphToBigWigRequires bedtoolsPerforms NormalizationNormalize to read depthOne optionScale = (#bps in genome)(#bp per read) x (# mapped reads)
15 Two most common platforms IGVLocally installedUCSC Genome BrowserUpload required
16 Visual inspection of each normalized replicate is critical…