Hi,

I was searching for how many reads are spanning on each gene then I performed mapping and downstream analyzing with tophat and bowtie. But in bowtie2 output there are many reads mapped on each genes in short distances of each other but when inspecting cuffmerge output (merged.gtf) I saw there is one or maximum 2 reads too far from each other

For example this is gene_id, start and end columns in merged.gtf, you see we have only 2 reads for SNC1 genes and each reads are far from each other or overlapping, how possible only two reads have been mapped on SNC1 gene? And if these are only mapped exon, from which part of tophat or cufflinks I can find the reads spanning on each gene please?

SNC1    87287    87388
SNC1    87502    87753
FRT2    92901    94487
SAW1    94653    95473
SAW1    94688    95473
HRA1    99306    99869
HRA1    99306    99869