Usage¶

cli¶

program designed for detecting cryptic exons

Needed file types:

bam file
genome reference
annotation file

cli <options> <command>

Options

--version¶: Show the version and exit.

--verbose¶: Show the verbose mode

build¶

build database for annotation file

build database of annotation file in order to use the database to annotate junctions reads later. this process is time-confusing so that you may need to prepare a cup of coffee! file of database named {prefix of annotation file}.db

cli build <options> GFF

Options

-o, --out-directory <path>¶

Default: .

Arguments

GFF¶: Required argument

detect¶

detect junction reads and scan cryptic exons

analysis following steps below:
detect junction reads in terms of bam file
annotate junction reads in terms of genome reference and annotation file
scan cryptic exons according to its definition

cli detect <options>

Options

-b, --bam <path>¶: Required The bam file (Bam or Sam format)

-r, --reference <path>¶: Required The reference fasta (.fna) file, which contains index file(*.fai)

-q, --quality <int>¶

The threshold to filter low quality reads

Default: 0

-o, --out <path>¶

The output file of detected cryptic exons

Default: cryptic_exons.bed

-db, --gffdb <path>¶: Required The database of annotation file

-c, --cutoff <int>¶

cutoff for filtering junction reads wth low depth during scanning cryptic exons

Default: 1

-oa, --out-ann <path>¶

The output file of annotated junction reads

Default: annotated_junctions.bed