1) So if an alignment works best with a gap, we consider the gap to be a deletion and vice versa for an insertion?
2) Maybe I'm missing something but this is all I found about insertions and deletions on the TopHat man page:
insertions.bed and deletions.bed. UCSC BED tracks of insertions and deletions reported by TopHat. Insertions.bed - chromLeft refers to the last genomic base before the insertion. Deletions.bed - chromLeft refers to the first genomic base of the deletion.
Maybe what you said is all there is to the insertions and deletions - that a high scoring alignment with a gap indicates the presence of a deletion in that region?
Could you be more specific and add some information? At least to me your question is unclear...
Sure - TopHat produces a deletions.bed and insertions.bed file.
1) How are these insertions and deletions identified?
2) When mapping reads to the genome, we allow for a certain number of mismatches and gaps - how do these relate to how tophat identifies deletions and insertions?