search

griffithlab / regtools

Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.
https://regtools.readthedocs.org
MIT License
121 stars 26 forks source link

invalid strand values after running junctions extract #166

Open Vishvak2000 opened 2 years ago

Vishvak2000 commented 2 years ago

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 "*".

image

Thanks, V

kcotto commented 1 year ago

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.