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 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, 10 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).  3 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.

       # 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. 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.