bwa aln [-n maxDiff] [-o maxGapO] [-e maxGapE] [-d nDelTail] [-i nIndelEnd] [-k maxSeedDiff] [-l seedLen] [-t nThrds] [-cRN] [-M misMsc] [-O gapOsc] [-E gapEsc] [-q trimQual] <in.db.fasta> <in.query.fq> > <out.sai>



-n NUM Maximum edit distance if the value is INT, or the fraction of missing alignments given 2% uniform base error rate if FLOAT. In the latter case, the maximum edit distance is automatically chosen for different read lengths. [0.04]

-o INT Maximum number of gap opens [1]

-e INT Maximum number of gap extensions, -1 for k-difference mode (disallowing long gaps) [-1]

-d INT Disallow a long deletion within INT bp towards the 3’-end [16]

-i INT Disallow an indel within INT bp towards the ends [5]

-l INT Take the first INT subsequence as seed. If INT is larger than the query sequence, seeding will be disabled. For long reads, this option is typically ranged from 25 to 35 for ‘-k 2’. [inf]

-k INT Maximum edit distance in the seed [2]

-t INT Number of threads (multi-threading mode) [1]

-M INT Mismatch penalty. BWA will not search for suboptimal hits with a score lower than (bestScore-misMsc). [3]

-O INT Gap open penalty [11]

-E INT Gap extension penalty [4]

-R INT Proceed with suboptimal alignments if there are no more than INT equally best hits. This option only affects paired-end mapping. Increasing this threshold helps to improve the pairing accuracy at the cost of speed, especially for short reads (~32bp).

-c Reverse query but not complement it, which is required for alignment in the color space. (Disabled since 0.6.x)

-N Disable iterative search. All hits with no more than maxDiffdifferences will be found. This mode is much slower than the default.

-q INTParameter for read trimming. BWA trims a read down to argmax_x{\sum_{i=x+1}^l(INT-q_i)} if q_l

-I The input is in the Illumina 1.3+ read format (quality equals ASCII-64).

-B INT Length of barcode starting from the 5’-end. When INT is positive, the barcode of each read will be trimmed before mapping and will be written at the BC SAM tag. For paired-end reads, the barcode from both ends are concatenated. [0]

-b Specify the input read sequence file is the BAM format. For paired-end data, two ends in a pair must be grouped together and options -1 or -2are usually applied to specify which end should be mapped. Typical command lines for mapping pair-end data in the BAM format are:

bwa aln ref.fa -b1 reads.bam > 1.sai 
bwa aln ref.fa -b2 reads.bam > 2.sai 
bwa sampe ref.fa 1.sai 2.sai reads.bam reads.bam > aln.sam

-0 When -b is specified, only use single-end reads in mapping.

-1 When -b is specified, only use the first read in a read pair in mapping (skip single-end reads and the second reads).

-2 When -b is specified, only use the second read in a read pair in mapping.

Protocols using this tool

Identifying RNA editing sites using RNA sequencing data alone

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