Bam file track:
In RNA-Seq bams, sometimes I can't see the actual reads because it displays all the bridging reads first (reads that begin in a previous exon and end in the next) and exons that are in the middle do not show any reads because it says "data exceeds limit". I would make 2 changes to this track, one if the read doesn't have any bases (only N's for example a typical cigar 54M203185N35M )and you are looking at the N's part you should be able to hide that. Second, high coverage areas do not display the variant bases (I'm guessing the object limit is triggered and then you don't see the changes). It would be nice if the system could randomly pick say 100 reads and map those so that you can look at snps.
from google community user:
Bam file track: In RNA-Seq bams, sometimes I can't see the actual reads because it displays all the bridging reads first (reads that begin in a previous exon and end in the next) and exons that are in the middle do not show any reads because it says "data exceeds limit". I would make 2 changes to this track, one if the read doesn't have any bases (only N's for example a typical cigar 54M203185N35M )and you are looking at the N's part you should be able to hide that. Second, high coverage areas do not display the variant bases (I'm guessing the object limit is triggered and then you don't see the changes). It would be nice if the system could randomly pick say 100 reads and map those so that you can look at snps.