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lecture-6-handouts - Practical Bioinformatics for Life...

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9/8/2011 1 Practical Bioinformatics for Life Scientists Week 3, Lecture 6 István Albert Bioinformatics Consulting Center Penn State A few UNIX tips Data for lecture 6 A subset of a fastq file obtained from an Illumina run for a Chip-Seq experiment with yeast DNA The annotation and genome file that we extracted in lecture 3 and 5 as well. ) Too keep things tidy create a new folder just for reference genomes, move the genome file there then index it with BWA (see lecture 5) SAM: Sequence Alignment/Map format Sequencing Reads Alignment Software SAM file Chip-Seq RNA-Seq SNPs
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9/8/2011 2 Create an alignment of only 10 sequences SAM format Published as The Sequence Alignment/Map format and SAMtools by Heng Li et al Bioinformatics 25, Volume 25, Issue 16, 2009 “A TAB-delimited text format consisting of a header section, which is optional, and an alignment section .” The structure of the SAM file Headers Alignments The alignment columns
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9/8/2011 3 A tour of the columns in a SAM file
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