.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
.TH SUBREAD-ALIGN "1" "June 2017" "subread-align 1.5.1+dfsg-4~bpo8+1" "User Commands"
.SH 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)
.SH USAGE

\fBsubread\-align\fR [options] \fB\-i\fR <index_name> \fB\-r\fR <input> \fB\-o\fR <output> \fB\-t\fR <type>
.PP
Required arguments:
.TP
\fB\-i\fR <string>
Base name of the index.
.TP
\fB\-r\fR <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.
.TP
\fB\-t\fR <int>
Type of input sequencing data. Its values include
0: RNA\-seq data
1: genomic DNA\-seq data.
.PP
Optional arguments:
.TP
\fB\-o\fR <string>
Name of the output file. By default, the output is in BAM
format.
.TP
\fB\-n\fR <int>
Number of selected subreads, 10 by default.
.TP
\fB\-m\fR <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. 3 by default
.TP
\fB\-M\fR <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.
.TP
\fB\-T\fR <int>
Number of CPU threads used, 1 by default.
.TP
\fB\-I\fR <int>
Maximum length (in bp) of indels that can be detected. 5 by
default. The program can detect indels of up to 200bp long.
.TP
\fB\-B\fR <int>
Maximal number of equally\-best mapping locations to be
reported. 1 by default. Note that \fB\-u\fR option takes precedence
over \fB\-B\fR.
.TP
\fB\-P\fR <3:6>
Format of Phred scores in input files, '3' for phred+33 and
\&'6' for phred+64. '3' by default.
.TP
\fB\-u\fR
Report uniquely mapped reads only. Number of matched bases (
for RNA\-seq) or mis\-matched bases(for genomic DNA\-seq) is
used to break the tie.
.TP
\fB\-b\fR
Convert color\-space read bases to base\-space read bases in
the mapping output. Note that read mapping is performed at
color\-space.
.TP
\fB\-\-sv\fR
Detect structural variants (eg. long indel, inversion,
duplication and translocation) and report breakpoints. Refer
to Users Guide for breakpoint reporting.
.TP
\fB\-\-SAMinput\fR
Input reads are in SAM format.
.TP
\fB\-\-BAMinput\fR
Input reads are in BAM format.
.TP
\fB\-\-SAMoutput\fR
Save mapping result in SAM format.
.TP
\fB\-\-trim5\fR <int>
Trim off <int> number of bases from 5' end of each read. 0
by default.
.TP
\fB\-\-trim3\fR <int>
Trim off <int> number of bases from 3' end of each read. 0
by default.
.TP
\fB\-\-rg\-id\fR <string>
Add read group ID to the output.
.TP
\fB\-\-rg\fR <string>
Add <tag:value> to the read group (RG) header in the output.
.TP
\fB\-\-DPGapOpen\fR <int> Penalty for gap opening in short indel detection. \fB\-1\fR by
default.
.TP
\fB\-\-DPGapExt\fR <int>
Penalty for gap extension in short indel detection. 0 by
default.
.TP
\fB\-\-DPMismatch\fR <int> Penalty for mismatches in short indel detection. 0 by
default.
.TP
\fB\-\-DPMatch\fR <int>
Score for matched bases in short indel detection. 2 by
default.
.TP
\fB\-\-complexIndels\fR
Detect multiple short indels that occur concurrently in a
small genomic region (these indels could be as close as 1bp
apart).
.TP
\fB\-v\fR
Output version of the program.
.PP
Optional arguments for paired\-end reads:
.TP
\fB\-R\fR <string>
Name of the file including second reads.
.TP
\fB\-p\fR <int>
Consensus threshold for the non\-anchor read (receiving less
votes than the anchor read from the same pair). 1 by
default.
.TP
\fB\-d\fR <int>
Minimum fragment/insert length, 50bp by default.
.TP
\fB\-D\fR <int>
Maximum fragment/insert length, 600bp by default.
.TP
\fB\-S\fR <ff:fr:rf>
Orientation of first and second reads, 'fr' by default (
forward/reverse).
.PP
Refer to Users Manual for detailed description to the arguments.