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changes.mady.by.user Benjamin M Goetz

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3. Align the fastq to the reference:

Code Block
bwa aln -f out.sai <reference.fasta> p1.<experiment name>.fastq  > out.sai 2> out.log&>bwa.log &

For colorspace,

Code Block
bwa aln -c -f out.sai <reference.fasta> p1.<experiment name>.fastq  > out.sai 2> out.log&>bwa.log &

If your reads are mate-pair, you must run this command once for your F3 reads and then again for your R3 reads, into seperate output files.

4. Convert the alignment output to a SAM file; the command required depends on whether data is paired-end or single-end:

Code Block
bwa sampe -f out.sam <reference.fasta> F3.sai F5.sai F3.fastq F5.fastq >&>bwa.sampe.log &
bwa -f out.sam bwa samse <reference.fasta> F3.sai F3.fastq > out.sam&>bwa.samse.log &

NOTE: these sam files contain ALL reads, whether they hit the reference or not which can make them LARGE.  To filter for just hits, use something like this:

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