USAGE

subjunc [options] -i <index_name> -r <input> -o <output>

Required arguments:

-i <index>

Base name of the index.

-r <string>

Name of the input file. Input formats including gzipped fastq, fastq, and fasta can be automatically detected. If paired-end, this should give the name of file including first reads.

Optional arguments:

-o <string>

Name of the output file. By default, the output is in BAM format.

-n <int>

Number of selected subreads, 14 by default.

-m <int>

Consensus threshold for reporting a hit (minimal number of subreads that map in consensus) . If paired-end, this gives the consensus threshold for the anchor read. 1 by default

-M <int>

Specify the maximum number of mis-matched bases allowed in the alignment. 3 by default. Mis-matches found in softclipped bases are not counted.

-T <int>

Number of CPU threads used, 1 by default.

-I <int>

Maximum length (in bp) of indels that can be detected. 5 by default. The program can detect indels of up to 200bp long.

-B <int>

Maximal number of equally-best mapping locations to be reported. 1 by default. Note that -u option takes precedence over -B.

-P <3:6>

Format of Phred scores used in input files, '3' for phred+33 and '6' for phred+64. '3' by default.

-u

Report uniquely mapped reads only. Number of mis-matched bases is used to break the tie.

-b

Convert color-space read bases to base-space read bases in the mapping output. Note that read mapping is performed at color-space.

--SAMinput

Input reads are in SAM format.

--BAMinput

Input reads are in BAM format.

--SAMoutput

Save mapping result in SAM format.

--trim5 <int>

Trim off <int> number of bases from 5' end of each read. 0 by default.

--trim3 <int>

Trim off <int> number of bases from 3' end of each read. 0 by default.

--rg-id <string>

Add read group ID to the output.

--rg <string>

Add <tag:value> to the read group (RG) header in the output.

--DPGapOpen <int> Penalty for gap opening in short indel detection. -1 by

default.

--DPGapExt <int>

Penalty for gap extension in short indel detection. 0 by default.

--DPMismatch <int> Penalty for mismatches in short indel detection. 0 by

default.

--DPMatch <int>

Score for matched bases in short indel detection. 2 by default.

--allJunctions

Detect exon-exon junctions (both canonical and non-canonical junctions) and structural variants in RNA-seq data. Refer to Users Guide for reporting of junctions and fusions.

--complexIndels

Detect multiple short indels that occur concurrently in a small genomic region (these indels could be as close as 1bp apart).

-v

Output version of the program.

Optional arguments for paired-end reads:

-R <string>

Name of the file including second reads.

-p <int>

Consensus threshold for the non-anchor read (receiving less votes than the anchor read from the same pair). 1 by default.

-d <int>

Minimum fragment/insert length, 50bp by default.

-D <int>

Maximum fragment/insert length, 600bp by default.

-S <ff:fr:rf>

Orientation of first and second reads, 'fr' by default ( forward/reverse).

Refer to Users Manual for detailed description to the arguments.