Usage and best practices

To be filled.

Recommendations regarding reference genome annotation

To be considered: https://github.com/hillerlab/TOGA/issues/49

Isoforms data

to be filled

U12 introns data

relevant issue

to be filled

Recommendations regarding genome alignments

to be filled

Using multiple references and queries

Pls see:

• About multiple references
• About multiple queries

Understanding logs

To be fixed in 1.1.5: Iter 4380 waiting 262800 seconds Not done is a confusing message showing that cesar jobs are still running (and nothing else) (https://github.com/hillerlab/TOGA/issues/51)