difference between tophat2 and bowtie2 alingner

Question

[zizigolu]

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

[GouthamAtla]

What "downstream analyzing with tophat and bowtie" did you do ? What is that table?

[zizigolu]

this is cut and paste three columns from merged.gtf from cufflikns , gene name, start and end of genes... I mean after mapping with bowte I converted sam to bam then bed and so on to extract the gene name and start and end which in tophat procedure I extracted from merged.gtf

[ATpoint]

It may not directly contribute to your question, but Tophat is deprecated and bowtie2 is not splice-aware. Go with HISAT2 to be up to date.