FATAL ERROR: cannot insert junctions on the fly because of strand GstrandBit problem

[Jason White]

Hi Alex,

All of my star runs are failing alignment with the same error:

EXITING because of FATAL ERROR: cannot insert junctions on the fly because of strand GstrandBit problem

SOLUTION: please contact STAR author at https://groups.google.com/forum/#!forum/rna-star

I looked through some of your replies to others with the same error but could not pin down a solution. Please look at the attached log file and let me know what you think. 

Thanks!

[Alexander Dobin]

Hi Jason,

since you are adding a very large number of junction (~7M), you would need to do it at the genome generation, specifying 
--limitSjdbInsertNsj 10000000 . This should solve the GstrandBit problem.

Such a large number of junctions may lead to a significant slowdown and increase in multi-mapping rate, so I generally recommend to filter the junctions to bring their number to <1M.

Cheers

Alex