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Introduction
HISAT2 is the fastest transcriptome-aware spliced mapper currently available. It is part of the new tuxedo suite of tools and it will map RNA-Seq data to the genome as well as identify splice junctions. HISAT2, like BWA and bowtie, uses burrows-wheeler transform (BWT) to compress genomes such that they require very little memory to store. Like BWA and bowtie, it builds indexes out of the transformed genomes using a special scheme called FM indexing. This makes it possible to search through these genomes rapidly. Unlike BWA and bowtie, HISAT2 builds a whole genome global index and tens of thousands of small local indexes to make spliced alignment possible. Despite the many indexes, because it uses BWT and FM indexing, the indexes take a very small memory footprint (~5gb RAM for the whole human genome), making it possible to run hisat2 on a standard laptop.
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As you can see, HISAT2 is not currently a module on stampede. When a program is not available on stampede, you can install it locally in your home or work directory. I have already installed HISAT in my work directory and since my work directory is in your path, you should be able to run hisat2. Type in hisat2 to see if it is in your path and to get usage information.
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hisat2 |
Part 1. Create a index of your reference
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3. Log file : The log file should contain alignment summaries.
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ls results head results/GSM794483_C1.sam head results/GSM794483_C1.junctions |
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11607353 reads; of these:
11607353 (100.00%) were paired; of these:
21592 (0.19%) aligned concordantly 0 times
11417720 (98.37%) aligned concordantly exactly 1 time
168041 (1.45%) aligned concordantly >1 times
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21592 pairs aligned concordantly 0 times; of these:
82 (0.38%) aligned discordantly 1 time
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21510 pairs aligned 0 times concordantly or discordantly; of these:
43020 mates make up the pairs; of these:
25009 (58.13%) aligned 0 times
9694 (22.53%) aligned exactly 1 time
8317 (19.33%) aligned >1 times
99.89% overall alignment rate |