Examples¶

diceseq demo¶

• Run diceseq for isoform proportions (add --add_premRNA if you want pre-mRNA as an extra transcript):

  • separated model

  anno_file=data/anno/yeast_RNA_splicing.gtf
  sam_dir=data/sam
  out_file=data/out/t1
  sam_list=$sam_dir/reads_t1.sorted.bam
  diceseq -a $anno_file -s $sam_list -o $out_file --add_premRNA
  

  • joint model

  out_file=data/out/joint
  sam_list=$sam_dir/reads_t1.sorted.bam---$sam_dir/reads_t2.sorted.bam---$sam_dir/reads_t3.sorted.bam
  diceseq -a $anno_file -s $sam_list -o $out_file --add_premRNA
  

dice-count demo¶

• Run dice-count for reads counts:

  • total count

  anno_file=data/anno/yeast_RNA_splicing.gtf
  sam_file=data/sam/reads_t3.sorted.bam
  out_file=data/out/t3_cnt1.txt
  dice-count -a $anno_file -s $sam_list -o $out_file
  

  • specific reads count, e.g., junctions (make sure it contains one intron only)

  out_file=data/out/t3_cnt2.txt
  dice-count  -a $anno_file -s $sam_list -o $out_file --junction
  

For more options, see the detailed usages page.