Output

Output

1. Standard output

The standard output format is a .tsv file.

Header	Interpretation
chr	Chromosome name
strand	Strand orientation
gene_ID	Ensembl gene ID
transcript_ID	Ensembl transcript ID
intron_ID	Intron ordinal position
sj5start	5' splice junction - start position
sj5end	5' splice junction - end position
sj5_cov_nonsplit	5' splice junction - unsplit reads coverage
sj5_cov_split	5' splice junction - split reads coverage
sj3start	3' splice junction - start position
sj3end	3' splice junction - end position
sj3_cov_nonsplit	3' splice junction - unsplit reads coverage
sj3_cov_split	3' splice junction - split reads coverage
SE	Splicing Efficiency

2. IER

The output format for --IERatio (-e) option is also a .tsv file.

Header	Interpretation
chr	Chromosome name
IStart	Intron start position
IEnd	Intron end position
strand	Strand orientation
intron_ID	Intron ordinal position
gene_ID	Ensembl gene ID
transcript_ID	Ensembl transcript ID
exon5_cov	Median per-base read coverage of the 5' exon
sj5_cov_split	5' splice junction - split reads coverage
sj5_cov_nonsplit	5' splice junction - unsplit reads coverage
intron_cov	Median per-base read coverage of the intron
sj3_cov_split	3' splice junction - split reads coverage
sj3_cov_nonsplit	3' splice junction - unsplit reads coverage
exon3_cov	Median per-base read coverage of the 3' exon
IER	Reverse Intron Expression Ratio