lecture-24-handouts

lecture-24-handouts - Compile wgsim get wgsim from GitHub...

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11/10/2011 1 Practical Bioinformatics for Life Scientists Week 12, Lecture 24 István Albert Bioinformatics Consulting Center Penn State Midterm project report: ReadSeq data format conversion Note: not all conversions are valid! Usually you can only go from a complex format to a simpler one. BWA vs Bowtie 1 vs Bowtie 2 Testing on simulated reads BWA and realistic ones bowtie For both sensitivity (mapping rate) and specificity (correct alignments) We’ll keep a score along the way We all need to remember: both tools are triumphs of human ingenuity! bowtie2 bwa bwa bowtie2 Short Read Archive Command line toolkit to convert from the sra format to fastq, ssf, csfasta formats
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11/10/2011 2 Clone the wgsim repository on github
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Unformatted text preview: Compile wgsim get wgsim from GitHub Install the bowties Cannot install on cygwin! Mac Linux only Building indices for each tool 11/10/2011 3 Running the aligners wgsim evaluation Quality reports get alignment reports Redirect standard error to output get alignment reports 11/10/2011 4 An R program to plot it bwa bowtie2 bowtie1 Homework 24 Install R (optionally Rstudio ) (will be using them during the next two lectures) Install and then run wgsim_eval.pl script on one of your SAM files that came from a wgsim simulator Inspect the CIGAR strings of reads that were classified incorrectly and see if there is a pattern to them...
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lecture-24-handouts - Compile wgsim get wgsim from GitHub...

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