STAR2bSMRT_NRXN: STAR2bSMRT_NRXN the main function of STAR2bSMRT specially...

In zhushijia/STAR2bSMRT: STARlong and STARshort based Single Molecule Real Time Iso-Seq analysis

Description

STAR2bSMRT_NRXN the main function of STAR2bSMRT specially designed for NRXN1 alpha splicing identification

Usage

STAR2bSMRT_NRXN(genomeDir, genomeFasta, LRphqv = NULL, LRflnc = NULL,
  LRnfl = NULL, SR1, SR2 = NULL, useSJout = TRUE,
  adjustNCjunc = FALSE, thresSR, thresDis, outputDir,
  fixedMatchedLS = FALSE, fuzzyMatch = 100, chrom = NULL, s = 0,
  e = Inf, cores = 10)

Arguments

genomeDir	character value indicating the directory of STAR genome index for both STARlong and STARshort read mapping
genomeFasta	character value indicating the fasta file of genome reference
SR1	character value indicating the short read file in fastq format: single-end or paired-end R1
SR2	character value indicating the short read file in fastq format: paired-end R2
useSJout	boolean value indicating whether to use the STARshort generated SJ.out.tab for splicing junction. If FALSE, STAR2bSMRT infer the splicing junction from bam files. By default, FALSE.
adjustNCjunc	boolean value indicating whether to minimize the non-canonical junction sites.
thresSR	a vector of integers indicating the searching range for the number of short reads which support the splicing junction sites.
thresDis	a vector of integers indicating the searching range for the tolerance distance between short read-derived splicing junction and long read-derived junction. STAR2bSMRT will correct the long read-derived junction to the short read-derived junction, if more short reads than defined thresSR support that short read-derived junction, and the distance between long and short read junctions is shorter than the defined thresDis.
outputDir	character value indicating the direcotry where results are saved.
fixedMatchedLS	boolean value indicating how often the distance is calculate betwen long read and short read-derived junction sites. If TRUE, only calculated once at the very beginning, which may save running time; otherwise, calculate repeatly after every long read correction. By default, FALSE.
fuzzyMatch	integer value indicating the distance for fuzzyMatch
chrom	character value indicating the chromosome of interest. By default, STAR2bSMRT works on the whole genome.
s	integeter value indicating the start position of the transcript of interest. This is useful for target Isoseq sequencing.
e	integeter value indicating the end position of the transcript of interest. This is useful for target Isoseq sequencing.
cores	integer value indicating the number of cores for parallel computing
phqv	character value indicating the Isoseq polished high QV trascripts in fasta/fastq, where read counts for each transcript consensus should be saved in transcript names
flnc	character value indicating the Isoseq full-length non-chimeric reads in fasta/fastq format
nfl	character value indicating the Isoseq non-full-length reads in fasta/fastq format

zhushijia/STAR2bSMRT documentation built on Dec. 18, 2019, 7:37 a.m.