Versions Compared

Old Version 10

changes.mady.by.user Dhivya Arasappan

Saved on

compared with

New Version 11

changes.mady.by.user Dhivya Arasappan

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

Code Block
titleLet's just take a look at the commands
$TACC_HTSEQ_DIR/scripts/htseq-count -m intersection-nonempty --stranded reverse -i gene_id C1_R1_thout/accepted_hits.sam reference/genes.formatted.gtf > C1_count1.gff 
$TACC_HTSEQ_DIR/scripts/htseq-count -m intersection-nonempty --stranded reverse -i gene_id C1_R2_thout/accepted_hits.sam reference/genes.formatted.gtf > C1_count2.gff 
$TACC_HTSEQ_DIR/scripts/htseq-count -m intersection-nonempty --stranded reverse -i gene_id C1_R3_thout/accepted_hits.sam reference/genes.formatted.gtf > C1_count3.gff 
$TACC_HTSEQ_DIR/scripts/htseq-count -m intersection-nonempty --stranded reverse -i gene_id C2_R1_thout/accepted_hits.sam reference/genes.formatted.gtf > C2_count4.gff 
$TACC_HTSEQ_DIR/scripts/htseq-count -m intersection-nonempty --stranded reverse -i gene_id C2_R2_thout/accepted_hits.sam reference/genes.formatted.gtf > C2_count5.gff 
$TACC_HTSEQ_DIR/scripts/htseq-count -m intersection-nonempty --stranded reverse -i gene_id C2_R3_thout/accepted_hits.sam reference/genes.formatted.gtf > C2_count6.gff 
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

...