The limit means that for the span where the red line is, only the first 5000 features sorted by start position, starting from the tile with the red line, is shown. That usually means it will cut off at some point midway through the tile.. it doesn't indicate that the blank part of the tile has no data. We're working on making this better so that you can at least see some data where the blank space is.

On Sat, Apr 30, 2011 at 5:28 PM, Jeremy Chien <Chien.Jeremy@mayo.edu> wrote:

Hi

During the visualization of my mRNAseq data, some area have red line
indicating that only the first 5000 reads are displayed. Within this
region, some area have many reads. Some area, where exons exist, I
don't see any reads. How do I interpret the data? If there are no
reads shown in the visualization, although there is a read line saying
only the first 5000 reads are displayed, does the absence of reads
corresponding to a particular exon means it is not expressed?

Thanks,
Jeremy

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