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| Code Block |
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| title | Get set up for the exercises |
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cds
cd my_rnaseq_course
cd day_1_partB2/hisat_exercise
ls |
Next, see if HISAT2 is a module that is available on lonestar5.
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module spider hisat |
As you can see, HISAT2 is not currently a module on lonestar5. When a program is not available on lonestar5, 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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module load biocontainers
module spider hisat2
module load python3/3.7.0
module load hisat2/ctr-2.1.0--py36pl5.22.0_0 |
Part 1. Create a index of your reference
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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 |
| Expand |
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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 -m " module load biocontainers; module load python3/3.7.0; module load hisat2/ctr-2.1.0--py36pl5.22.0_0" |
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Hisat2 output
1.SAM file : HISAT2 alignment output in standard SAM format.
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