I prepared a small RNA (28-34nt) library made up of ribosome protected RNA fragments. I prepared my library for illumina sequencing by RT-PCR and adaptor ligation.
Results were excellent with ~3-4M reads per each indexed data set, six total, very high QC results.
After adaptor trimming and size selection of >28nt; Bowtie alignment of my reads to a rabbit genome (oryCun2) gives me 53% alignment with 51% aligned >1 time. This sample is a mixture of rabbit and human as it is a cell free translation reaction of huCFTR. Perhaps some of the alignments are missed at the intron exon boundaries.
If I display these BAM files on the UCSC main will I be looking at all possible alignments or a single best alignment for each read?