I've a little question on sam and bam file sizes.
When I use bwa on paired-end reads (~50M reads) on a small reference sequence (~100 kb) , I've a bam file of about 5 Go . After looking the alignment, only a few reads aligned on this reference (~500 reads max)
But When I use tophat with the same input and the same reference, the output bam has a size of only 10 kb and the number of aligned reads is the same...
So is it a way to reduce my bam file ?