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Bowtie2 is a complete rewrite of bowtie. It is currently the latest and greatest in the eyes of one very picky instructor (and his postdoc/gradstudent) in terms of configurability, sensitivity, and speed. After years of teaching bwa mapping along with bowtie2, last year was the first class to use only bowtie2 since we never recommend anyone use bwa, and based on positive feedback we continue with this set up. For some more details about the differences between them see the how read mappers work see the bonus presentation, and if you find a compelling reason to use bwa (or any other read mapper) rather than bowtie2, we'd love to hear from you.
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- SAM files can be enormously humongous text files (potentially >1 gigabytes). Attempting to open the entire file at once can cause your computer to lock up or your text editor to crash. You are generally safer only looking at a portion at a time using linux commands like
headorgrepor more or using a viewer like IGV, which we will cover later. - SAM files have some rather complicated information encoded as text, like a binary encoded FLAGS field and CIGAR strings. We'll take a look at some of these later, if we have time, or they are covered in the bonus tutorialpresentation.
Still, you should recognize some of the information on a line in a SAM file from the input FASTQ, and some of the other information is relatively straightforward to understand, like the position where the read mapped. Give this a try:
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