Page Comparison

nano commands.htseq
 
#put these lines in the commands file
htseq-count -m intersection-nonempty --stranded reverse -i gene_id hisat_results/C1_R1.sam ../reference/genes.formatted.gtf > C1_count1.gff 
htseq-count -m intersection-nonempty --stranded reverse -i gene_id hisat_results/C1_R2.sam ../reference/genes.formatted.gtf > C1_count2.gff 
htseq-count -m intersection-nonempty --stranded reverse -i gene_id hisat_results/C1_R3.sam ../reference/genes.formatted.gtf > C1_count3.gff 
htseq-count -m intersection-nonempty --stranded reverse -i gene_id hisat_results/C2_R1.sam ../reference/genes.formatted.gtf > C2_count4.gff 
htseq-count -m intersection-nonempty --stranded reverse -i gene_id hisat_results/C2_R2.sam ../reference/genes.formatted.gtf > C2_count5.gff 
htseq-count -m intersection-nonempty --stranded reverse -i gene_id hisat_results/C2_R3.sam ../reference/genes.formatted.gtf > C2_count6.gff 

launcher_creator.py -j commands.htseq -n htseq -q normal -t 02:00:00 -a OTH21164 -l htseq_launcher.slurm
-m "module load htseq"
sbatch --reservation=RNAseq htseq_launcher.slurm

join C1_count1.gff C1_count2.gff| join - C1_count3.gff | join - C2_count4.gff |join - C2_count5.gff|join - C2_count6.gff > gene_counts_HTseq.gff

#if you have many samples, use for-loop and join