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As you can imagine from this series of steps, Tophat is very computationally intensive and takes much longer than bwa mem – very large alignments (hundreds of millions of reads) may not complete in stampede's 48 hour maximum job time!
Exercise #5: Simple
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SAMtools Utilities
We have used several alignment methods that all generate results in the form of the near-universal SAM/BAM file format. The samtools The SAMtools program is an extremely widespread ubiquitously used set of tools that allow a user to manipulate SAM/BAM files in many different ways, ranging from simple tasks (like converting SAM to BAM (and vice versa/BAM interconversion) to more complex functions (like the removal of PCR duplicates or the filtering of alignments by various metrics). It is available in the TACC module system in the typical fashion. In this exercise, we will explore three use five very simple utilities provided by samtools, each of which takes only one line to fully run: view, sort, index, flagstat, and idxstats. Each of these is executed in one line for a given SAM/BAM file. In the next SAMtools/BEDtools section, we will explore samtools much more in depth, and show how it can be connected to other post-alignment tools..
For the sake of time and simplicity, here we are only going to run these commands on the yeast paired-end alignment file. However, the exact same commands can be run on the other files by changing the names, so feel free to try executing the same commands on other SAM files. Indeed, it is very common in practice to use bash loops to generate many commands for a large set of alignments and deposit those commands into a batch job cmds file for submission.
Samtools Sort
Samtools View
Samtools Index
Samtools Idxstats
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