tophat functionality

[cswarth]

I really don't understand why tophat has such a sparse set of command-line options for controlling alignment while bowtie's options are so rich. Bowtie lets me control the quality of alignment and how many alignments are reported for a given read. Bowtie allows me to trim reads from either 5' or 3' end on the command-line. Tophat doesn't allow for any control of how many reads are reported or what quality scores are acceptable, or what gets trimmed.

The real question is, are there any tools that allow junction spanning alignment (based on a junction annotation file) but which also output at most a single alignment for each read, and even better, will tell me what gene a read is aligned against?

Is there a way to run bowtie by hand that ends up with the same junction-spanning alignments that tophat produces, but with more control?

Thanks in advance,

- Chris

[holywoool]

Althouth based on bowtie,TopHat concentrates in junction finding and several options from bowtie are enough.TopHat does have a -g option which is the same as -m in bowtie.