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First, the longer part of a read that maps to the genome contiguously (called the anchor) is mapped using the global index. Once this is mapped, this helps to to identify the relevant local index. HISAT can usually align the remaining part of the read (small anchor) within a single local index rather than searching across the whole genome.
Run HISAT2
First, make sure you are in the right directory for this exercise.
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Warning |
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title | Submit to the TACC queue or run in an idev shell |
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Create a commands file and use launcher_creator.py followed by sbatch. Code Block |
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title | Put this in your commands file |
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| nano commands.hisat2
hisat2 -x ../reference/genome.fa -1 ../data/GSM794483_C1_R1_1.fq -2 ../data/GSM794483_C1_R1_2.fq -S GSM794483_C1.sam --phred33 --novel-splicesite-outfile GSM794483_C1.junctions --rna-strandness RF --dta -t
hisat2 -x ../reference/genome.fa -1 ../data/GSM794484_C1_R2_1.fq -2 ../data/GSM794484_C1_R2_2.fq -S GSM794484_C1.sam --phred33 --novel-splicesite-outfile GSM794484_C1.junctions --rna-strandness RF --dta -t
hisat2 -x ../reference/genome.fa -1 ../data/GSM794485_C1_R3_1.fq -2 ../data/GSM794485_C1_R3_2.fq -S GSM794485_C1.sam --phred33 --novel-splicesite-outfile GSM794485_C1.junctions --rna-strandness RF --dta -t
hisat2 -x ../reference/genome.fa -1 ../data/GSM794486_C2_R1_1.fq -2 ../data/GSM794486_C2_R1_2.fq -S GSM794486_C1.sam --phred33 --novel-splicesite-outfile GSM794486_C1.junctions --rna-strandness RF --dta -t
hisat2 -x ../reference/genome.fa -1 ../data/GSM794487_C2_R2_1.fq -2 ../data/GSM794487_C2_R2_2.fq -S GSM794487_C1.sam --phred33 --novel-splicesite outfile GSM794487_C1.junctions --rna-strandness RF --dta -t
hisat2 -x ../reference/genome.fa -1 ../data/GSM794488_C2_R3_1.fq -2 ../data/GSM794488_C2_R3_2.fq -S GSM794488_C1.sam --phred33 --novel-splicesite-outfile GSM794488_C1.junctions --rna-strandness RF --dta -t |
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title | Use this Launcher_creator command |
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| launcher_creator.py -n hisat2 -t 01:00:00 -j commands.hisat2 -q normal -a UT-2015-05-18 -l hisat2_launcher.slurm -N 6 |
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Hisat2 output
1.SAM file : HISAT2 alignment output in standard SAM format.
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Code Block |
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title | Example alignment summary |
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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 |
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