Tophat Junctions Search Via Segment Mapping.

Question

[Fernando Rossello]

Hi Guys,

I understand that BowTie alignments can be multithread and the no. of processors can be defined. However, is there any way of multithreading the search for junctions via segment mapping step (segment_juncs process) in TopHat?

Thanks in advance.

Fernando

Answer 1

[Damian Kao]

The only multi-threaded process in tophat is when it uses multiple instances of bowtie to map reads. There is no option to turn on multi-threading for the data shuffling/parsing steps like segment_juncs.

Segment_juncs is basically used to parse the left/right fragment mappings to find more potential splice sites. You might be able to modify the program to make it multi-thread depending on the algorithm it uses to find potential splice sites.

If it looks at each read fragment mappings individually, then you could potentially just run multiple instances of segment_juncs and feed them chunks of the correspinding left/right segment mappings.

But I think it is more likely that it looks at all the fragment mappings in a holistic way to find potential junctions. In that case, I don't think it can be multi-threaded.

[Fernando Rossello]

Thanks DK. This answers my question.