Basic bowtie2 alignment notes

It’s equally been a while since I’ve driven bowtie, and now there’s bowtie2. Basic alignment notes:

./bowtie2-build ~/genomics/myreferece.fasta myreference
./bowtie2 -x myreference -q myreads.fastq -S ./al.sam

And out pops a SAM file. This can be converted to a BAM with samtools:

./samtools faidx ~/genomics/myreference.fasta
./samtools import ~/genomics/myreference.fasta.fai ./al.sam ./al.bam