invalid strand values after running junctions extract

[Vishvak2000]

Hello,

I am trying to run regtools junctions extract -s 1 on my bam file - I get an output however the strand column contains "?" instead of "-" or "*".

Thanks,
V

[kcotto]

We've now changed the strandedness option to use more traditional values like RF, FR, etc instead of numbers like 0, 1, 2. Additionally, we now have an option that you can use -C that will use information in the fasta file to try to assign strandedness to reads. More information here: https://regtools.readthedocs.io/en/latest/commands/cis-splice-effects-identify/

Please let me know if you continue to have issues.