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

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Practical Bioinformatics for Life Scientists Week 3, Lecture 6 István Albert Bioinformatics Consulting Center Penn State
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A few UNIX tips
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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)
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SAM: Sequence Alignment/Map format Sequencing Reads Alignment Software SAM file Chip-Seq RNA-Seq SNPs
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Create an alignment of only 10 sequences
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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 .”
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The structure of the SAM file Headers Alignments
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The alignment columns
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A tour of the columns in a SAM file We will go through each field in class
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Bitwise flags
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