I have recently mapped RNA-seq reads to the sacCer2 genome using bowtie in galaxy. I then filtered the SAM file for reads that mapped. Then I converted to bam and clicked the link to visualize in the UCSC browser. My question is will every single read be displayed in the UCSC browser or does it randomly select a certain percentage of reads to visualize? I ask because sometimes it looks like there are fewer reads than expected based upon a separate calculation of how many reads should overlap with a given gene. When there is a small enough number that I can count it appears to match up but when it's more than 50 reads it looks like some reads are being left out.