Usage¶
cli¶
program designed for detecting cryptic exons
Needed file types:
1. bam file
2. genome reference
3. 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:
1. detect junction reads in terms of bam file
2. annotate junction reads in terms of genome reference and annotation file
3. scan cryptic exons according to its definition
cli detect <options>
Options
-
-b,--bam<path>¶ Required The bam file (Bam or Sam format)
-
-q,--quality<int>¶ The threshold to filter low quality reads
- Default
30
-
-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
-
--parallel¶ using parallel mode