NAME

       subjunc - an RNA-seq aligner suitable for all purposes of RNA-seq analyses

USAGE

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

       ## Mandatory arguments:

       -i <index>
              Base name of the index.

       -r <string>
              Name  of  an  input  read  file.  If  paired-end,  this  should  be the first read file (typically
              containing "R1"in the file name) and the second should be provided via "-R".   Acceptable  formats
              include   gzipped   FASTQ,   FASTQ,  gzipped  FASTA  and  FASTA.   These  formats  are  identified
              automatically.

       ## Optional arguments: # input reads and output

       -o <string>
              Name of an output file. By default, the output is in BAM format. Omitting this  option  makes  the
              output be written to STDOUT.

       -R <string>
              Name of the second read file in paired-end data (typically containing "R2" the file name).

       --SAMinput
              Input reads are in SAM format.

       --BAMinput
              Input reads are in BAM format.

       --SAMoutput
              Save mapping results in SAM format.

       # Phred offset

       -P <3:6>
              Offset  value  added  to  the  Phred quality score of each read base. '3' for phred+33 and '6' for
              phred+64. '3' by default.

       # thresholds for mapping

       -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 (anchor read receives more
              votes than the other read in the same pair).  1 by default.

       -p <int>
              Consensus threshold for the non- anchor read in a pair. 1 by default.

       -M <int>
              Maximum number of mis-matched bases allowed in each reported alignment. 3 by default.  Mis-matched
              bases found in softclipped bases are not counted.

       # unique mapping and multi-mapping

       --multiMapping
              Report  multi-mapping  reads  in  addition  to  uniquely mapped reads. Use "-B" to set the maximum
              number of equally-best alignments to be reported.

       -B <int>
              Maximum number of equally-best alignments to be reported for a  multi-mapping  read.  Equally-best
              alignments have the same number of mis-matched bases. 1 by default.

       # indel detection

       -I <int>
              Maximum  length  (in  bp) of indels that can be detected. 5 by default. Indels of up to 200bp long
              can be detected.

       --complexIndels
              Detect multiple short indels that are in close proximity (they can be as close as 1bp  apart  from
              each other).

       # read trimming

       --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.

       # distance and orientation of paired end reads

       -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).

       # number of CPU threads

       -T <int>
              Number of CPU threads used, 1 by default.

       # read group

       --rg-id <string>
              Add read group ID to the output.

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

       # read order

       --keepReadOrder
              Keep order of reads in BAM output the same as that in the input file. Reads from the same pair are
              always placed next to each other no matter this option is specified or not.

       --sortReadsByCoordinates Output location-sorted reads. This option is
              applicable for BAM output only. A BAI index file is also generated for each BAM file  so  the  BAM
              files can be directly loaded into a genome browser.

       # color space reads

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

       # dynamic programming

       --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.

       # detect all junctions including gene fusions

       --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.

       # gene annotation

       -a     Name  of  an annotation file (gzipped file is accepted).  GTF/GFF format by default. See -F option
              for more format information.

       -F     Specify format of the provided annotation file. Acceptable formats include  'GTF'  (or  compatible
              GFF format) and 'SAF'. 'GTF' by default. For SAF format, please refer to Users Guide.

       -A     Provide  a  chromosome  name  alias file to match chr names in annotation with those in the reads.
              This should be a twocolumn comma-delimited text file. Its first column should include chr names in
              the  annotation  and  its  second column should include chr names in the index. Chr names are case
              sensitive. No column header should be included in the file.

       --gtfFeature <string>
              Specify feature type in GTF annotation. 'exon' by default. Features used for read counting will be
              extracted from annotation using the provided value.

       --gtfAttr <string>
              Specify  attribute  type  in  GTF  annotation.  'gene_id'  by default. Meta-features used for read
              counting will be extracted from annotation using the provided value.

       # others

       -v     Output version of the program.

       Refer to Users Manual for detailed description to the arguments.