Is there an option in bowtie to get a list of reads that did not align to the reference. Thanks
If you used bowtie with default settings, the unaligned reads should be present in the output (SAM) file. You can use "samtools view -f4" command to extract unmapped reads. You can then convert bam to fastq file or simply get the read names. Read the samtools manual for more help.
A: How To Filter Mapped Reads With Samtools