Producing sjdbFileChrStartEnd to add noncanonical junctions

[Ryan Englander]

Hi Dr. Dobin,

I am trying to use --sjdbFileChrStartEnd to add candidate noncanonical junctions I am interested in as annotations prior to the mapping step. I obtained these junctions via a prior --twoPassMode Basic run, however, and so I do not know the strand orientation.

What do I put on the final column of the -sjdbFileChrStartEnd *.tab if I do not know the strand? Can STAR handle this, or should I just add the junction as both a + and a - on separate lines? Thanks so much!

Kindest regards,

Ryan Englander

[Alexander Dobin]

Hi Ryan,

For unknown strand, you can use . (dot) symbol.

Cheers

Alex