SJanalysis: Splice Junction (SJ) analysis

In wyguo/RTDBox: High resolution Transcriptome using Single Molecule PacBio Iso-seq data

Splice Junction (SJ) analysis

Description

Splice Junction (SJ) analysis

Usage

SJanalysis(
  input_dir,
  output_dir = NULL,
  genome_fasta = NULL,
  sj_overhang = 10,
  sjdatabase = NULL
)

Arguments

input_dir	The data directory of TAMA output
output_dir	The directory to save results
genome_fasta	The name of genome fasta sequence file. If the file is not in the working directory, please provide the full path.
sj_overhang	An integer of SJ overhang. A SJ is filtered if it has mismatches at its left (-sj_overhang) or right (+sj_overhang) exonic regions.
sjdatabase	A tab separated file of splice junction information. If a canonical SJ in the isoseq assembly has a match in the database, it will be kept even though it has mismatches in the overhangs.

Value

Results are saved in data_di

wyguo/RTDBox documentation built on Jan. 31, 2023, 1:19 a.m.