NAME

       subread-align  -  an accurate and efficient aligner for mapping both genomic DNA-seq reads
       and RNA-seq reads (for the purpose of expression analysis)

USAGE

       subread-align [options] -i <index_name> -r <input> -t <type> -o <output>

       ## Mandatory arguments:

       -i <string>
              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.

       -t <int>
              Type  of  input  sequencing  data.  Its  values  include 0: RNA-seq data 1: genomic
              DNA-seq data.

       ## 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.

       # 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 structural variants

       --sv   Detect   structural   variants   (eg.   long   indel,  inversion,  duplication  and
              translocation)  and  report  breakpoints.  Refer  to  Users  Guide  for  breakpoint
              reporting.

       # 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.