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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 1 |
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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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