how can we use the tophat deletions output?
e.g. if I want to see and conpare between two samples if a specific
gene or transcript had been deleted, how can I use this output?
is visualisation enough?
The file is described in the TopHat manual:
Along with the insertion files, deletions describes variation between
the query and the reference genome at the base level (nucleotide). It
does not describe whole transcripts or genes.
How to use this information is really up to you. This is very large
popular topic area with more information then I could outline in a
simple email reply. Even in Galaxy there are many tools and data
complete with descriptions and help and links to even more resources.
More of these are under active development.
The base way to start is with some research: Galaxy searches in the
panel, Pages, Workflows, Tool Shed, the Wiki, Galaxy custom google
searches or even just a plain Google with keywords like "SNP" or
"Variation" or "Indel" or similar, alone or in combination, should get
you going, if this interests you.