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Code Block
titleLet's just take a look at the commands
$TACC_HTSEQ_DIR/scripts/htseq-count -m intersection-nonempty -i gene_id C1_R1_thout/accepted_hits.sam reference/genes.formatted.gtf > count1.gff 
$TACC_HTSEQ_DIR/scripts/htseq-count -m intersection-nonempty -i gene_id C1_R2_thout/accepted_hits.sam reference/genes.formatted.gtf > count2.gff 
$TACC_HTSEQ_DIR/scripts/htseq-count -m intersection-nonempty -i gene_id C1_R3_thout/accepted_hits.sam reference/genes.formatted.gtf > count3.gff 
$TACC_HTSEQ_DIR/scripts/htseq-count -m intersection-nonempty -i gene_id C2_R1_thout/accepted_hits.sam reference/genes.formatted.gtf > count4.gff 
$TACC_HTSEQ_DIR/scripts/htseq-count -m intersection-nonempty -i gene_id C2_R2_thout/accepted_hits.sam reference/genes.formatted.gtf > count5.gff 
$TACC_HTSEQ_DIR/scripts/htseq-count -m intersection-nonempty -i gene_id C2_R3_thout/accepted_hits.sam reference/genes.formatted.gtf > count6.gffgff 

 joinjoin count1.gff count2.gff| join - count3.gff | join - count4.gff |join - count5.gff|join - count6.gff > gene_counts_HTseq.gff
#if you have many samples, use for-loop and join

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