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

Info iconThis preview shows pages 1–10. Sign up to view the full content.

View Full Document Right Arrow Icon

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
This is the end of the preview. Sign up to access the rest of the document.

Unformatted text preview: 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 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 A tour of the columns in a SAM file We will go through each field in class Bitwise flags...
View Full Document

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.

Page1 / 16

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

This preview shows document pages 1 - 10. Sign up to view the full document.

View Full Document Right Arrow Icon
Ask a homework question - tutors are online