SEQanswers - BWA - input files

Hi,

I am trying to align paired end reads (Illumina) to a reference genome using BWA. I have 10 reads files, 5 for each direction.

In this old post 'totalnew' says to align the files separately:

Code:

bwa aln database.fasta 4_1.fq > 1_1.fq.sai

bwa aln database.fasta 4_2.fq > 1_2.fq.sai

bwa aln database.fasta 5_1.fq > 2_1.fq.sai

bwa aln database.fasta 5_2.fq > 2_2.fq.sai

[...]

I have been reading for quite a while now so sorry if I missed something totally obvious but how do I run sampe from there on? Can I just say

Code:

bwa sampe database.fa 1_1.fq.sai 2_1.fq.sai 3_1... 1_2.fq.sai 2_2.fq.sai 3_2... 1_1.fq 2_1.fq 3_1... 1_2.fq 2_2.fq 3_2... > alignment.sam

or do I need to run sampe for each file separately?
What if I concatenate all reads files into s_1_sequence.txt and s_2_sequences.txt and then run bwa aln twice and bwa samse once?

cheers!

ps (offtopic) @lh3: I tried downloading bwa 0.5.8a but it seems as though there are files missing. Here what I get:

Code:

wget http://sourceforge.net/projects/bio-bwa/files/bwa-0.5.8a.tar.bz2/download

bunzip2 bwa-0.5.8a.tar.bz2

tar -xf bwa-0.5.8a.tar

ls bwa-0.5.8a

bntseq.c  bwase.c     bwtaln.c  bwtgap.h    bwtio.c     bwtsw2_aux.c    bwtsw2_main.c  is.c     kstring.c  main.h        simple_dp.c     utils.c

bntseq.h  bwase.h     bwtaln.h  bwt_gen     bwt_lite.c  bwtsw2_chain.c  ChangeLog      khash.h  kstring.h  Makefile      solid2fastq.pl  utils.h

bwa.1     bwaseqio.c  bwt.c     bwt.h       bwt_lite.h  bwtsw2_core.c   COPYING        kseq.h   kvec.h     NEWS          stdaln.c

bwape.c   bwa.txt     bwtgap.c  bwtindex.c  bwtmisc.c   bwtsw2.h        cs2nt.c        ksort.h  main.c     qualfa2fq.pl  stdaln.h

I downloaded 0.5.7 and it runs fine.