USAGE
subread-align [options] -i <index_name> -r <input> -o <output> -t <type>
Required arguments:
- -i <string>
- 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.
- -t <int>
- Type of input sequencing data. Its values include 0: RNA-seq data 1: genomic DNA-seq data.
Optional arguments:
- -o <string>
- Name of the output file. By default, the output is in BAM format.
- -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. 3 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 in input files, '3' for phred+33 and '6' for phred+64. '3' by default.
- -u
- 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.
- -b
- Convert color-space read bases to base-space read bases in the mapping output. Note that read mapping is performed at color-space.
- --sv
- Detect structural variants (eg. long indel, inversion, duplication and translocation) and report breakpoints. Refer to Users Guide for breakpoint reporting.
- --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.
- --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.