[Useq-users] How to speedup the process of building junction library

[michael xu <mic...@gm...>]

Hi David,

Thank you for developing a very useful tool USeq!

I am using the USeq to build a novoalign index file with junction library,
but I found it takes a very long time (> 5+ hours or longer) to build a
junction library.
Until now, I still have not finish one junction library for human 19 on a
very powerful cluster.
Do you have any suggestion on how to build a junction library quickly?

Besides, I know I can download a library from your website with 50nt, but
the length of read in my dataset is 51nt. I am not sure if I can use the
same junction library build by you even the length of read is 51nt. Suppose
that -r should set "length of read - 4".

Your response would be greatly appreciated!

Michael