lecture-8-handouts - 9/15/2011 Reminder Practical...

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1 Practical Bioinformatics for Life Scientists Week 4, Lecture 8 István Albert Bioinformatics Consulting Center Penn State Reminder Before any serious work re-check the documentation for small but essential details. Example: bwa needs to be indexed differently for small and large genomes bwa has to be invoked with different alignment modes for short reads (200 < ) and long reads (200 >) Sequencing Coverage (Depth) Lander/Waterman model: 1. random reads 2. ability to detect overlap does not change coverage C = N * L / G N = number of reads, L = length of reads, G = size of genome Probability of a base not being sequenced P = exp(-C) To get the percent of genome not covered (multiply by 100) N=35 million, L=35, G=250 million C = 5 0.6% genome not sequenced 15 million bases not covered Realistic coverage Neither of the models assumptions are correct multiply required coverage at least 10 fold What part of the genome is coverable to begin with? Also known as
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This note was uploaded on 02/29/2012 for the course BMMB 597D taught by Professor Istvanalbert during the Fall '11 term at Pennsylvania State University, University Park.

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lecture-8-handouts - 9/15/2011 Reminder Practical...

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