Using bwa dbwtsw

[freeseek]

Hi would like to know how can I use bwa to align the reads using the standard aln method with the command:

bwa aln database.fasta short_read.fastq > aln_sa.sai

and then use it again to align the unaligned reads with the dbwtsw Smith-Waterman-like alignment. Is there an easy way to extract from the .fastq+.sai files the list of reads that did not align?

[lh3]

bwasw and aln/sampe/samse are different algorithms. To use bwasw:

bwa bwasw ref.fa long-read.fastq

To get alignments from .sai:

bwa sampe/samse

Unmapped reads are also in the output.

[rafi bondi]

how can i remove the unmapped reads?

[nilshomer]

use "samtools view -F 4"