Content Comparison

nano commands.bedtools

#enter below commands into the file
singularity exec ${BIOCONTAINER_DIR}/biocontainers/bedtools/bedtools-2.27.1--1.simg bedtools multicov -bams hisat_results/C1_R1.sorted.bam hisat_results/C1_R2.sorted.bam hisat_results/C1_R3.sorted.bam hisat_results/C2_R1.sorted.bam hisat_results/C2_R2.sorted.bam hisat_results/C2_R3.sorted.bam -bed ../reference/genes.formatted.gtf > gene_counts.gff 
 
#use ctrl+x to quit out of nano

launcher_creator.py -j commands.bedtools -n multicov -q normal -t 02:00:00 -a OTH21164 -l bedtools_launcher.slurm -m "module load xalt;module load biocontainers; module load bedtools"
sbatch --reservation=RNAseqrna-seq-class-0611 bedtools_launcher.slurm    

nano commands.express
 
#put these commands into the file
singularity exec ${BIOCONTAINER_DIR}/biocontainers/express/express-1.5.1--h2d50403_1.simg express -o C1_R1_counts.express ../reference/transcripts.fasta hisat../../day_2/bwa_exercise/bwa_mem_results_transcriptome/C1_R1.mem.samsa
singularity exec ${BIOCONTAINER_DIR}/biocontainers/express/express-1.5.1--h2d50403_1.simg express -o C1_R2_counts.express ../reference/transcripts.fasta hisat../../day_2/bwa_exercise/bwa_mem_results_transcriptome/C1_R2.mem.sam
singularity exec ${BIOCONTAINER_DIR}/biocontainers/express/express-1.5.1--h2d50403_1.simg express -o C1_R3_counts.express ../reference/transcripts.fasta hisat../../day_2/bwa_exercise/bwa_mem_results_transcriptome/C1_R3.mem.sam
singularity exec ${BIOCONTAINER_DIR}/biocontainers/express/express-1.5.1--h2d50403_1.simg express -o C2_R1_counts.express ../reference/transcripts.fasta hisat../../day_2/bwa_exercise/bwa_mem_results_transcriptome/C2_R1.mem.sam
singularity exec ${BIOCONTAINER_DIR}/biocontainers/express/express-1.5.1--h2d50403_1.simg express -o C2_R2_counts.express ../reference/transcripts.fasta hisat../../day_2/bwa_exercise/bwa_mem_results_transcriptome/C2_R2.mem.sam
singularity exec ${BIOCONTAINER_DIR}/biocontainers/express/express-1.5.1--h2d50403_1.simg express -o C2_R3_counts.express ../reference/transcripts.fasta hisat../../day_2/bwa_exercise/bwa_mem_results_transcriptome/C2_R3.mem.sam 

launcher_creator.py -j commands.express -n express -q normal -t 04:00:00 -a OTH21164 -l express_launcher.slurm -m "module load xalt;module load biocontainers;module load express"
sbatch --reservation=rna-seq-class-0611 express_launcher.slurm